Optimal maize loci

ABSTRACT

As disclosed herein, optimal native genomic loci from maize plants have been identified that represent best sites for targeted insertion of exogenous sequences.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No. 14/531,739, filed Nov. 3, 2014, which claims the benefit, under 35 U.S.C. § 119(e), to U.S. Provisional Patent Application No. 61/899,598, filed on Nov. 4, 2013, the contents of which are incorporated by reference in their entirety into the present application.

REFERENCE TO SEQUENCE LISTING SUBMITTED ELECTRONICALLY

The official copy of the sequence listing is submitted electronically via EFS-Web as an ASCII formatted sequence listing with a file named “279930_SEQ_LIST_ST25.txt,” created on Aug. 13, 2018, and having a size of 13 megabytes and is filed concurrently with the specification. The sequence listing contained in this ASCII formatted document is part of the specification and is herein incorporated by reference in its entirety.

REFERENCE TO TABLE LISTING SUBMITTED ELECTRONICALLY

The official copy of the table listing is submitted electronically via EFS-Web as a .PDF formatted table listing with a file named “Table 3”, created on Nov. 4, 2013, and having a size of 8.32 megabytes and is filed concurrently with the specification. The table listing contained in this .PDF formatted document is part of the specification and is herein incorporated by reference in its entirety.

BACKGROUND

The maize genome was successfully transformed with transgenes in the early 1990's. Over the last twenty years, numerous methodologies have been developed for transforming the maize genome, wherein a transgene is stably integrated into the maize genome. This evolution of maize transformation methodologies has resulted in the capability to successfully introduce a transgene comprising an agronomic trait within the maize genome. The introduction of insect resistance and herbicide tolerant traits within maize plants in the late—1990's provided producers with a new and convenient technological innovation for controlling insects and a wide spectrum of weeds, which was unparalleled in cultivation farming methods. Currently, transgenic maize is commercially available throughout the world, and new transgenic maize products such as Enlist™ Corn offer improved solutions for ever-increasing weed challenges. The utilization of transgenic maize in modern agronomic practices would not be possible, but for the development and improvement of maize transformation methodologies.

However, current maize transformation methodologies rely upon the random insertion of transgenes within the maize genome. Reliance on random insertion of genes into a genome has several disadvantages. The transgenic events may randomly integrate within gene transcriptional sequences, thereby interrupting the expression of endogenous traits and altering the growth and development of the maize plant. In addition, the transgenic events may indiscriminately integrate into locations of the corn genome that are susceptible to gene silencing, culminating in the reduced or complete inhibition of transgene expression either in the first or subsequent generations of transgenic maize plants. Finally, the random integration of transgenes within the maize genome requires considerable effort and cost in identifying the location of the transgenic event and selecting transgenic events that perform as designed without agronomic impact to the plant. Novel assays must be continually developed to determine the precise location of the integrated transgene for each transgenic event, such as a maize event. The random nature of maize transformation methodologies results in a “position-effect” of the integrated transgene, which hinders the effectiveness and efficiency of maize transformation methodologies.

Targeted genome modification of plants has been a long-standing and elusive goal of both applied and basic research. Targeting genes and gene stacks to specific locations in the Zea mays genome will improve the quality of transgenic events, reduce costs associated with production of transgenic events and provide new methods for making transgenic plant products such as sequential gene stacking. Overall, targeting transgenes to specific genomic sites is likely to be commercially beneficial. Significant advances have been made in the last few years towards development of methods and compositions to target and cleave genomic DNA by site specific nucleases (e.g., Zinc Finger Nucleases (ZFNs), Meganucleases, Transcription Activator-Like Effector Nucleases (TALENS) and Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated nuclease (CRISPR/Cas) with an engineered crRNA/tracr RNA), to induce targeted mutagenesis, induce targeted deletions of cellular DNA sequences, and facilitate targeted recombination of an exogenous donor DNA polynucleotide within a predetermined genomic locus. See, for example, U.S. Patent Publication No. 20030232410; 20050208489; 20050026157; 20050064474; and 20060188987, and International Patent Publication No. WO 2007/014275, the disclosures of which are incorporated by reference in their entireties for all purposes. U.S. Patent Publication No. 20080182332 describes use of non-canonical zinc finger nucleases (ZFNs) for targeted modification of plant genomes and U.S. Patent Publication No. 20090205083 describes ZFN-mediated targeted modification of a plant EPSPs genomic locus. Current methods for targeted insertion of exogenous DNA typically involve co-transformation of plant tissue with a donor DNA polynucleotide containing at least one transgene and a site specific nuclease (e.g., ZFN) which is designed to bind and cleave a specific genomic locus of an actively transcribed coding sequence. This causes the donor DNA polynucleotide to stably insert within the cleaved genomic locus resulting in targeted gene addition at a specified genomic locus comprising an actively transcribed coding sequence.

An alternative approach is to target the transgene to preselected target nongenic loci within the corn genome. In recent years, several technologies have been developed and applied to plant cells for the targeted delivery of a transgene within the corn genome. However, much less is known about the attributes of genomic sites that are suitable for targeting. Historically, non-essential genes and pathogen (viral) integration sites in genomes have been used as loci for targeting. The number of such sites in genomes is rather limiting and there is therefore a need for identification and characterization of targetable optimal genomic loci that can be used for targeting of donor polynucleotide sequences. In addition to being amenable to targeting, optimal genomic loci are expected to be neutral sites that can support transgene expression and breeding applications. A need exists for compositions and methods that define criteria to identify optimal nongenic loci within the corn genome for targeted transgene integration.

SUMMARY

In accordance with one embodiment a recombinant sequence is provided comprising an optimal nongenic maize genomic sequence and an exogenous sequence, wherein the exogenous sequence is inserted into the optimal nongenic maize genomic sequence. In an embodiment, the subject disclosure relates to a recombinant sequence, comprising: a nucleic acid sequence of at least 1 Kb and having at least 90%, 95%, or 99% sequence identity with a nongenic sequence selected from the group consisting of loci_137693_G1 (SEQ ID NO:387), loci_265551_G1 (SEQ ID NO:463), loci_128078_G1 (SEQ ID NO:560), loci_168286_G1 (SEQ ID NO:573), loci_3733_G1 (SEQ ID NO:1268), loci_203075_G1 (SEQ ID NO:2030), loci_232484_G1 (SEQ ID NO:2053), loci_136086_G1 (SEQ ID NO:4425), loci_203704_G1 (SEQ ID NO:2033), loci_127268_G1 (SEQ ID NO:2709), loci_204637_G1 (SEQ ID NO:2731), loci_291068_G1 (SEQ ID NO:3230), loci_232222_G1 (SEQ ID NO:3357), loci_43577_G1 (SEQ ID NO:3428), loci_204726_G1 (SEQ ID NO:424), loci_232228_G1 (SEQ ID NO: 4529) with a DNA of interest inserted into the nongenic sequence. In one embodiment, the insertion of the DNA of interest into the optimal nongenic maize genomic sequence modifies the original sequence of the nongenic loci by alterations of the nongenic loci sequence proximal to the insertion site. Such modifications include, for example, deletions, inversions, insertions, and duplications of the nongenic loci sequence. In a further aspect, an embodiment relates to a DNA of interest, wherein the DNA of interest is inserted into said nongenic sequence. In another aspect, an embodiment comprises the recombinant sequence, wherein a DNA of interest is inserted proximal to a zinc finger target site of Table 8. In another aspect, an embodiment comprises the recombinant sequence, wherein a DNA of interest is inserted at a zinc finger target site of Table 8. In another embodiment, the recombinant sequence comprises an inserted DNA of interest that further comprises an analytical domain. In another embodiment, the recombinant sequence comprises an inserted DNA of interest that does not encode a peptide. In a further embodiment, the recombinant sequence comprises a DNA of interest that encodes a peptide. In yet another embodiment, the recombinant sequence comprises an inserted DNA of interest that further comprises a gene expression cassette. In an embodiment, the gene expressions cassette contains a gene comprising an insecticidal resistance gene, herbicide tolerance gene, nitrogen use efficiency gene, water use efficiency gene, nutritional quality gene, DNA binding gene, and selectable marker gene. In a further embodiment, the recombinant sequence comprises two or more gene expression cassettes. In another embodiment, the recombinant sequence comprises two or more of said nongenic sequences each comprise an inserted DNA of interest to produce two or more recombinant sequences wherein the two or more recombinant sequences that are located on a same chromosome. In an additional embodiment, the recombinant sequence comprises the DNA of interest and/or the nongenic sequence are modified during insertion of said DNA of interest into the nongenic sequence. In another embodiment, the subject disclosure relates to a maize plant, maize plant part, or maize plant cell comprising a recombinant sequence comprising a nucleic acid sequence of at least 1 Kb and having at least 90%, 95%, or 99% sequence identity with a nongenic sequence selected from the group consisting of loci_137693_G1 (SEQ ID NO:387), loci_265551_G1 (SEQ ID NO:463), loci_128078_G1 (SEQ ID NO:560), loci_168286_G1 (SEQ ID NO:573), loci_3733_G1 (SEQ ID NO:1268), loci_203075_G1 (SEQ ID NO:2030), loci_232484_G1 (SEQ ID NO:2053), loci_136086_G1 (SEQ ID NO:4425), loci_203704_G1 (SEQ ID NO:2033), loci_127268_G1 (SEQ ID NO:2709), loci_204637_G1 (SEQ ID NO:2731), loci_291068_G1 (SEQ ID NO:3230), loci_232222_G1 (SEQ ID NO:3357), loci_43577_G1 (SEQ ID NO:3428), loci_204726_G1 (SEQ ID NO:424), loci_232228_G1 (SEQ ID NO: 4529) with a DNA of interest inserted into the nongenic sequence.

In a further embodiment, the disclosure relates to a method of making a transgenic plant cell comprising a DNA of interest. In another aspect of the disclosure, the method comprises selecting a target nongenic maize genomic locus having at least 90%, 95%, or 99% sequence identity with a target nongenic maize genomic locus selected from the group consisting of loci_137693_G1 (SEQ ID NO:387), loci_265551_G1 (SEQ ID NO:463), loci_128078_G1 (SEQ ID NO:560), loci_168286_G1 (SEQ ID NO:573), loci_3733_G1 (SEQ ID NO:1268), loci_203075_G1 (SEQ ID NO:2030), loci_232484_G1 (SEQ ID NO:2053), loci_136086_G1 (SEQ ID NO:4425), loci_203704_G1 (SEQ ID NO:2033), loci_127268_G1 (SEQ ID NO:2709), loci_204637_G1 (SEQ ID NO:2731), loci_291068_G1 (SEQ ID NO:3230), loci_232222_G1 (SEQ ID NO:3357), loci_43577_G1 (SEQ ID NO:3428), loci_204726_G1 (SEQ ID NO:424), and loci_232228_G1 (SEQ ID NO: 4529); selecting a site specific nuclease that specifically binds and cleaves said target nongenic maize genomic locus; introducing said site specific nuclease into a maize plant cell; introducing the DNA of interest into the plant cell; inserting the DNA of interest into said target nongenic maize genomic loci; and, selecting transgenic plant cells comprising the DNA of interest targeted to said nongenic locus. In a further aspect, an embodiment relates to a method of making a transgenic plant cell. In another embodiment, the DNA of interest comprises an analytical domain. In an embodiment, the DNA of interest does not encode a peptide. In yet another embodiment, the DNA of interest encodes a peptide. In a further embodiment, the DNA of interest comprises a gene expression cassette comprising a transgene. In another embodiment, the DNA of interest comprises two or more gene expression cassettes. In a subsequent embodiment, the site specific nuclease is selected from the group consisting of a zinc finger nuclease, a CRISPR nuclease, a TALEN, a homing endonuclease or a meganuclease. In an embodiment, the DNA of interest is integrated within said nongenic locus via a homology directed repair integration method. In another embodiment, the DNA of interest is integrated within said nongenic locus via a non-homologous end joining integration method. In a further embodiment, the method of making a transgenic plant cell provides for two or more of said DNA of interest that are inserted into two or more of said target nongenic maize genomic loci. In another embodiment, the method of making a transgenic plant cell comprises two or more of said target nongenic maize genomic loci that are located on a same chromosome. In an additional embodiment, the method of making a transgenic plant cell comprises the DNA of interest and/or the nongenic sequence that are modified during insertion of said DNA of interest into the nongenic sequence.

In accordance with one embodiment, a purified maize polynucleotide loci is disclosed herein, wherein the purified sequence comprises a nongenic sequence of at least 1 Kb. In one embodiment the nongenic sequence is hypomethylated, exemplifies evidence of recombination and is located in proximal location to an expressing genic region in the maize genome. In one embodiment, the nongenic sequence has a length ranging from about 1 Kb to about 8.4 Kb. In one embodiment, the DNA of interest comprises exogenous DNA sequences, including for example regulatory sequences, restriction cleavage sites, RNA encoding regions or protein encoding regions. In one embodiment, the DNA of interest comprises a gene expression cassette comprising one or more transgenes. In another embodiment, the purified sequence comprises a nongenic sequence having at least 90%, 95%, or 99% sequence identity with a nongenic sequence selected from the group consisting of loci_137693_G1 (SEQ ID NO:387), loci_265551_G1 (SEQ ID NO:463), loci_128078_G1 (SEQ ID NO:560), loci_168286_G1 (SEQ ID NO:573), loci_3733_G1 (SEQ ID NO:1268), loci_203075_G1 (SEQ ID NO:2030), loci_232484_G1 (SEQ ID NO:2053), loci_136086_G1 (SEQ ID NO:4425), loci_203704_G1 (SEQ ID NO:2033), loci_127268_G1 (SEQ ID NO:2709), loci_204637_G1 (SEQ ID NO:2731), loci_291068_G1 (SEQ ID NO:3230), loci_232222_G1 (SEQ ID NO:3357), loci_43577_G1 (SEQ ID NO:3428), loci_204726_G1 (SEQ ID NO:424), and loci_232228_G1 (SEQ ID NO: 4529). In a further embodiment, the purified nongenic maize genomic loci comprise a DNA of interest, wherein said DNA of interest is inserted into said nongenic sequence. In another aspect, an embodiment comprises the purified nongenic maize genomic loci, wherein said DNA of interest is inserted proximal to a zinc finger target site of Table 8. In a different aspect, an embodiment comprises the purified nongenic maize genomic loci, wherein said DNA of interest is inserted between a pair of zinc finger target sites selected from Table 8. In yet another aspect, an embodiment comprises the purified nongenic maize genomic loci and a DNA of interest inserted into the nongenic maize genomic loci, wherein said DNA of interest comprises an analytical domain. In another aspect, an embodiment comprises the purified recombinant nongenic maize genomic loci, wherein said DNA of interest does not encode a peptide. In a subsequent aspect, an embodiment comprises the purified recombinant nongenic maize genomic loci, wherein said DNA of interest encodes a peptide. In an embodiment, the purified recombinant nongenic maize genomic loci comprises a gene expression cassette, wherein the gene cassette comprises a gene including, for example, an insecticidal resistance gene, herbicide tolerance gene, nitrogen use efficiency gene, water use efficiency gene, nutritional quality gene, DNA binding gene, and selectable marker gene. In one embodiment a DNA of interest is inserted into the nongenic maize genomic loci using a site specific nuclease wherein the site specific nuclease is selected from the group consisting of a zinc finger nuclease, a CRISPR nuclease, a TALEN, a homing endonuclease or a meganuclease. In an embodiment, the said DNA of interest is integrated within said nongenic sequence via a homology directed repair integration method. In another embodiment, the said DNA of interest is integrated within said nongenic sequence via a non-homologous end joining integration method. In a further embodiment, the DNA of interest comprises two or more gene expression cassettes. In a further embodiment, two or more of DNA of interest are inserted into two or more of said target nongenic maize genomic loci. In one embodiment, two or more of said target nongenic maize genomic loci are provided wherein each comprise an inserted DNA of interest to produce two or more recombinant sequences wherein the said target nongenic maize genomic loci are located on a same chromosome. In an additional embodiment, the purified nongenic maize genomic comprises the DNA of interest and/or the nongenic sequence that are modified during insertion of said DNA of interest into the nongenic sequence. In another embodiment, the DNA of interest is inserted via a homology directed repair or a non-homologous end joining repair mechanism.

In another embodiment, the subject disclosure provides for a plant comprising a recombinant sequence, said recombinant sequence comprising: a DNA of interest and a nucleic acid sequence having at least 90%, 95%, or 99% sequence identity with a nongenic sequence, wherein the DNA of interest is inserted into said nongenic sequence. In another embodiment, the nongenic sequence is selected from the group consisting of loci_137693_G1 (SEQ ID NO:387), loci_265551_G1 (SEQ ID NO:463), loci_128078_G1 (SEQ ID NO:560), loci_168286_G1 (SEQ ID NO:573), loci_3733_G1 (SEQ ID NO:1268), loci_203075_G1 (SEQ ID NO:2030), loci_232484_G1 (SEQ ID NO:2053), loci_136086_G1 (SEQ ID NO:4425), loci_203704_G1 (SEQ ID NO:2033), loci_127268_G1 (SEQ ID NO:2709), loci_204637_G1 (SEQ ID NO:2731), loci_291068_G1 (SEQ ID NO:3230), loci_232222_G1 (SEQ ID NO:3357), loci_43577_G1 (SEQ ID NO:3428), loci_204726_G1 (SEQ ID NO:424), and loci_232228_G1 (SEQ ID NO: 4529). In an additional embodiment, the plant comprises two or more of said recombinant sequences. In a further embodiment the plant comprises two recombinant sequences that are located on the same chromosome. In another embodiment the plant comprises a DNA of interest inserted proximal to a zinc finger target site of Table 8. In one embodiment the plant comprises a DNA of interest inserted between a pair of zinc finger target sites selected from Table 8. In an embodiment, said DNA of interest comprises an analytical domain. In a further embodiment, said DNA of interest does not encode a peptide. In yet another embodiment, said DNA of interest encodes a peptide. In a subsequent embodiment, said DNA of interest comprises a gene expression cassette encoding a gene product, including for example, an insecticidal resistance gene, herbicide tolerance gene, nitrogen use efficiency gene, water use efficiency gene, nutritional quality gene, DNA binding gene, and selectable marker gene. In another embodiment the plant comprises a DNA of interest and/or a nongenic sequence that are modified during insertion of said DNA of interest into said nongenic sequence.

In an embodiment, the subject disclosure relates to a recombinant sequence, comprising: a nucleic acid sequence of at least 1 Kb and having at least 90%, 95%, or 99% sequence identity with a nongenic sequence selected from the group consisting of loci_137693_G1 (SEQ ID NO:387), loci_203075_G1 (SEQ ID NO:2030), and loci_204637_G1 (SEQ ID NO:2731), with a DNA of interest inserted into the nongenic sequence.

In an embodiment, the subject disclosure relates to a recombinant sequence, comprising: a nucleic acid sequence of at least 1 Kb and having at least 90%, 95%, or 99% sequence identity with a nongenic sequence selected from the group consisting of loci_265551_G1 (SEQ ID NO:463), loci_128078_G1 (SEQ ID NO:560), loci_168286_G1 (SEQ ID NO:573), loci_3733_G1 (SEQ ID NO:1268), and loci_232484_G1 (SEQ ID NO:2053), with a DNA of interest inserted into the nongenic sequence.

In an embodiment, the subject disclosure relates to a recombinant sequence, comprising: a nucleic acid sequence of at least 1 Kb and having at least 90%, 95%, or 99% sequence identity with a nongenic sequence selected from the group consisting of loci_127268_G1 (SEQ ID NO:2709), loci_232222_G1 (SEQ ID NO:3357), and loci_204726_G1 (SEQ ID NO:424), with a DNA of interest inserted into the nongenic sequence.

In an embodiment, the subject disclosure relates to a recombinant sequence, comprising: a nucleic acid sequence of at least 1 Kb and having at least 90%, 95%, or 99% sequence identity with a nongenic sequence selected from the group consisting of loci_136086_G1 (SEQ ID NO:4425), loci_203704_G1 (SEQ ID NO:2033), loci_291068_G1 (SEQ ID NO:3230), loci_43577_G1 (SEQ ID NO:3428), and loci_232228_G1 (SEQ ID NO: 4529) with a DNA of interest inserted into the nongenic sequence.

In an embodiment, the subject disclosure relates to a recombinant sequence, comprising: a nucleic acid sequence of at least 1 Kb and having at least 90%, 95%, or 99% sequence identity with a nongenic sequence selected from the group consisting of loci_137693_G1 (SEQ ID NO:387), loci_265551_G1 (SEQ ID NO:463), loci_128078_G1 (SEQ ID NO:560), loci_168286_G1 (SEQ ID NO:573), loci_3733_G1 (SEQ ID NO:1268), loci_203075_G1 (SEQ ID NO:2030), loci_232484_G1 (SEQ ID NO:2053), and loci_204637_G1 (SEQ ID NO:2731), with a DNA of interest inserted into the nongenic sequence.

In an embodiment, the subject disclosure relates to a recombinant sequence, comprising: a nucleic acid sequence of at least 1 Kb and having at least 90%, 95%, or 99% sequence identity with a nongenic sequence selected from the group consisting of loci_137693_G1 (SEQ ID NO:387), loci_265551_G1 (SEQ ID NO:463), loci_128078_G1 (SEQ ID NO:560), loci_168286_G1 (SEQ ID NO:573), loci_3733_G1 (SEQ ID NO:1268), loci_203075_G1 (SEQ ID NO:2030), loci_232484_G1 (SEQ ID NO:2053), loci_127268_G1 (SEQ ID NO:2709), loci_204637_G1 (SEQ ID NO:2731), loci_232222_G1 (SEQ ID NO:3357), and loci_204726_G1 (SEQ ID NO:424), with a DNA of interest inserted into the nongenic sequence.

In an embodiment, the subject disclosure relates to a recombinant sequence, comprising: a nucleic acid sequence of at least 1 Kb and having at least 90%, 95%, or 99% sequence identity with a nongenic sequence selected from the group consisting of loci_136086_G1 (SEQ ID NO:4425), loci_203704_G1 (SEQ ID NO:2033), loci_127268_G1 (SEQ ID NO:2709), loci_291068_G1 (SEQ ID NO:3230), loci_232222_G1 (SEQ ID NO:3357), loci_43577_G1 (SEQ ID NO:3428), loci_204726_G1 (SEQ ID NO:424), and loci_232228_G1 (SEQ ID NO: 4529) with a DNA of interest inserted into the nongenic sequence.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1. Illustrates a screen-shot sample of a wiggle plot for the DNA methylation profile of root and shoot tissues obtained from Zea mays c.v. B73 chromosome number 1.

FIG. 2. Illustrates a distribution of the polynucleotide sequence lengths of the resulting hypomethylated genomic locations of the Zea mays c.v. B73 genome.

FIG. 3. Represents a three dimensional graph of the 5,286 optimal maize loci. The Principal Component Analysis (PCA) statistical approach was used to cluster the set of 5,286 identified optimal genomic loci into 32 distinct clusters based on their feature values (see Example 1). During the PCA process, five principal components (PC) were generated, with the top three PCs containing about 90% of the total variation in the dataset. These top three PCAs were used to graphically represent the 32 clusters in a three dimensional plot as shown in FIG. 3.

FIG. 4. Provides a schematic drawing indicating the chromosomal distribution of the 81 optimal genomic loci, and their relative positions on the maize chromosomes.

FIG. 5. Provides a graph showing the coverage of the 72 optimal genomic loci within Zea mays c.v. B104 and c.v.Hi-II genomic databases that were selected for targeting validation.

FIG. 6. Provides a schematic drawing indicating the Zea mays chromosomal location of 72 optimal genomic loci selected for targeting validation.

FIG. 7. Provides a plasmid map of pDAB111845 (SEQ ID NO:5418). The numbered elements (i.e., 5, 7, 8, 9, 10, 11, 12, 15, 16, 25, and 26) correspond with zinc finger nuclease binding sequences of about 20 to 35 base pairs in length that are recognized and cleaved by corresponding zinc finger nuclease proteins. These zinc finger binding sequences and the annotated “UZI Sequence” (which is a 100-150 bp template region containing restriction sites and DNA sequences for primer design or coding sequences) comprise the universal donor cassette.

FIG. 8. Representation of the universal donor polynucleotide sequence for integration via non-homologous end joining (NHEJ). Two proposed vectors are provide wherein a DNA of interest (DNA X) comprises one or more (i.e., “1-N”) zinc finger binding sites (ZFN BS) at either end of the DNA of interest. Vertical arrows show unique restriction sites and horizontal arrows represent potential PCR primer sites.

FIG. 9. Representation of the universal donor polynucleotide sequence for integration via homologous-directed repair (HDR). A DNA of interest (DNA X) comprising two regions of homologous sequences (HA) flanking the DNA of interest with zinc finger nuclease binding sites (ZFN) bracketing the DNAX and HA sequences. Vertical arrows show unique restriction sites and horizontal arrows represent potential PCR primer sites.

FIG. 10A-10C. Illustrates the constructs used for targeting and validation of the universal donor polynucleotide system integration within the Zea mays optimal genomic loci targeting and validation. FIG. 10A) ZFN design space with location of the ZFN pairs as previously shown in pDAB111845 of FIG. 5. The ZFN pairs are labeled numerically and correspond with specific ZFN binding sequences that are specifically recognized by ZFN proteins for binding and cleavage. FIG. 10B) Configuration of the ZFN expression construct. The ZFN expression construct contains a constitutive plant promoter (Zm Ubi1) which is used to drive expression of the ZFN protein. The ZFN protein contains the nuclear localization sequence (NLS), the zinc finger proteins (ZFP-L and ZFP-R, where L indicates left hand binding ZFN protein and R indicates right hand binding protein), Fok-1 endonuclease (Fok1) and the self-hydrolyzing 2A (2A). FIG. 10C) universal donor polynucleotide for NHEJ mediated targeting of Zea mays optimal genomic loci. Z1-Z6 represent ZFN binding sites specific for a Zea mays optimal genomic loci target. The number of ZFN sites can vary from 3-6. Vertical arrows show unique restriction sites and horizontal arrows represent potential PCR primer sites. The universal donor polynucleotide system is a short (110 bp) sequence that is common to donors used for integration within Zea mays optimal genomic loci.

FIG. 11. Plasmid map of pDAB8393.

FIG. 12. ZFN cleavage activity at Zea mays selected genomic loci targets. Cleavage activity is represented as number of sequences with indels (insertions and deletions) at the ZFN cleavage site per 1 million high quality reads.

FIG. 13. Validation of Zea mays selected genomic loci targets using NHEJ based Rapid Targeting Analysis (RTA) method.

FIGS. 14A-14B. Plasmid constructs transformed into Zea mays via random integration that comprise the events used for flanking sequence analysis and transgene expression studies. Randomly integrated maize transformation events were generated by transformation with the pDAB105817 (FIG. 14A) and pEPS1027 (FIG. 14B) plasmids containing the aad-1 transgene.

FIG. 15. Plasmid map of pDAB111846 (SEQ ID NO:5419). The numbered elements (i.e., 1, 2, 5, 6, 11, 12, 15, 16, 21, 22, 29 and 30) correspond with zinc finger nuclease binding sequences of about 20 to 35 base pairs in length that are recognized and cleaved by corresponding zinc finger nuclease proteins. These zinc finger binding sequences and the annotated “UZI Sequence” (which is a 100-150 bp template region containing restriction sites and DNA sequences for primer design or coding sequences) comprise the universal donor cassette.

FIG. 16. Plasmid map of pDAB117415 (SEQ ID NO:5420). The numbered elements (i.e., ZFN51 and ZFN52) correspond with zinc finger nuclease binding sequences of about 20 to 35 base pairs in length that are recognized and cleaved by corresponding zinc finger nuclease proteins. These zinc finger binding sequences and the annotated “UZI Sequence” (which is a 100-150 bp template region containing restriction sites and DNA sequences for primer design or coding sequences) comprise the universal donor cassette. Further included in this plasmid design is the “104113 Overlap” which are sequences that share homology to the plasmid vector for high throughput assembly of the universal donor cassettes within a plasmid vector (i.e., via Gibson assembly).

FIG. 17. Plasmid map of pDAB117416 (SEQ ID NO:5421). The numbered elements (i.e., ZFN54 and ZFN53) correspond with zinc finger nuclease binding sequences of about 20 to 35 base pairs in length that are recognized and cleaved by corresponding zinc finger nuclease proteins. These zinc finger binding sequences and the annotated “UZI Sequence” (which is a 100-150 bp template region containing restriction sites and DNA sequences for primer design or coding sequences) comprise the universal donor cassette. Further included in this plasmid design is the “104113 Overlap” which are sequences that share homology to the plasmid vector for high throughput assembly of the universal donor cassettes within a plasmid vector (i.e., via Gibson assembly).

FIG. 18. Plasmid map of pDAB117417 (SEQ ID NO:5422). The numbered element (i.e., ZFN55) correspond with zinc finger nuclease binding sequences of about 20 to 35 base pairs in length that are recognized and cleaved by corresponding zinc finger nuclease proteins. These zinc finger binding sequences and the annotated “UZI Sequence” (which is a 100-150 bp template region containing restriction sites and DNA sequences for primer design or coding sequences) comprise the universal donor cassette. Further included in this plasmid design is the “104113 Overlap” which are sequences that share homology to the plasmid vector for high throughput assembly of the universal donor cassettes within a plasmid vector (i.e., via Gibson assembly).

FIG. 19. Plasmid map of pDAB117419 (SEQ ID NO:5423). The numbered elements (i.e., ZFN59 and ZFN60) correspond with zinc finger nuclease binding sequences of about 20 to 35 base pairs in length that are recognized and cleaved by corresponding zinc finger nuclease proteins. These zinc finger binding sequences and the annotated “UZI Sequence” (which is a 100-150 bp template region containing restriction sites and DNA sequences for primer design or coding sequences) comprise the universal donor cassette. Further included in this plasmid design is the “104113 Overlap” which are sequences that share homology to the plasmid vector for high throughput assembly of the universal donor cassettes within a plasmid vector (i.e., via Gibson assembly).

FIG. 20. Plasmid map of pDAB117434 (SEQ ID NO:5424). The numbered elements (i.e., ZFN66, ZFN67, ZFN68 and ZFN69) correspond with zinc finger nuclease binding sequences of about 20 to 35 base pairs in length that are recognized and cleaved by corresponding zinc finger nuclease proteins. These zinc finger binding sequences and the annotated “UZI Sequence” (which is a 100-150 bp template region containing restriction sites and DNA sequences for primer design or coding sequences) comprise the universal donor cassette. Further included in this plasmid design is the “104113 Overlap” which are sequences that share homology to the plasmid vector for high throughput assembly of the universal donor cassettes within a plasmid vector (i.e., via Gibson assembly).

FIG. 21. Plasmid map of pDAB117418 (SEQ ID NO:5425). The numbered elements (i.e., ZFN56, ZFN57, and ZFN58) correspond with zinc finger nuclease binding sequences of about 20 to 35 base pairs in length that are recognized and cleaved by corresponding zinc finger nuclease proteins. These zinc finger binding sequences and the annotated “UZI Sequence” (which is a 100-150 bp template region containing restriction sites and DNA sequences for primer design or coding sequences) comprise the universal donor cassette. Further included in this plasmid design is the “104113 Overlap” which are sequences that share homology to the plasmid vector for high throughput assembly of the universal donor cassettes within a plasmid vector (i.e., via Gibson assembly).

FIG. 22. Plasmid map of pDAB117420 (SEQ ID NO:5426). The numbered elements (i.e., ZFN61 and ZFN62) correspond with zinc finger nuclease binding sequences of about 20 to 35 base pairs in length that are recognized and cleaved by corresponding zinc finger nuclease proteins. These zinc finger binding sequences and the annotated “UZI Sequence” (which is a 100-150 bp template region containing restriction sites and DNA sequences for primer design or coding sequences) comprise the universal donor cassette. Further included in this plasmid design is the “104113 Overlap” which are sequences that share homology to the plasmid vector for high throughput assembly of the universal donor cassettes within a plasmid vector (i.e., via Gibson assembly).

FIG. 23. Plasmid map of pDAB117421 (SEQ ID NO:5427). The numbered elements (i.e., PPL17 Pair 3, PPL17 Pair 1, and PPL17 Pair2) correspond with zinc finger nuclease binding sequences of about 20 to 35 base pairs in length that are recognized and cleaved by corresponding zinc finger nuclease proteins. These zinc finger binding sequences and the annotated “UZI Sequence” (which is a 100-150 bp template region containing restriction sites and DNA sequences for primer design or coding sequences) comprise the universal donor cassette. Further included in this plasmid design is the “104113 Overlap” which are sequences that share homology to the plasmid vector for high throughput assembly of the universal donor cassettes within a plasmid vector (i.e., via Gibson assembly).

FIGS. 24A-24C. Histogram of characteristics (length, expression of coding region within 40 Kb of loci, and recombination frequency) for the identified optimal nongenic maize loci. FIG. 24A illustrates a distribution of the polynucleotide sequence lengths of the optimal genomic loci (OGL). FIG. 24B illustrates the distribution of expressed nucleic acid sequences relative to their proximity (log scale) to the optimal genomic loci (OGL). FIG. 24C illustrates the distribution of the optimal nongenic maize loci relative to their recombination frequency.

FIGS. 25A-25B are histograms of characteristics (distance to actively transcribed endogenous gene and distance from centromere) for the identified optimal nongenic maize loci. FIG. 25A illustrates the distribution of the optimal genomic loci sequences relative to their distance to actively transcribed endogenous genes. FIG. 25B illustrates the distribution of the optimal genomic loci sequences relative to their distance to the chromosomal centromere.

DETAILED DESCRIPTION Definitions

In describing and claiming the invention, the following terminology will be used in accordance with the definitions set forth below.

The term “about” as used herein means greater or lesser than the value or range of values stated by 10 percent, but is not intended to designate any value or range of values to only this broader definition. Each value or range of values preceded by the term “about” is also intended to encompass the embodiment of the stated absolute value or range of values.

As used herein, the term “plant” includes a whole plant and any descendant, cell, tissue, or part of a plant. The term “plant parts” include any part(s) of a plant, including, for example and without limitation: seed (including mature seed and immature seed); a plant cutting; a plant cell; a plant cell culture; a plant organ (e.g., pollen, embryos, flowers, fruits, shoots, leaves, roots, stems, and explants). A plant tissue or plant organ may be a seed, callus, or any other group of plant cells that is organized into a structural or functional unit. A plant cell or tissue culture may be capable of regenerating a plant having the physiological and morphological characteristics of the plant from which the cell or tissue was obtained, and of regenerating a plant having substantially the same genotype as the plant. In contrast, some plant cells are not capable of being regenerated to produce plants. Regenerable cells in a plant cell or tissue culture may be embryos, protoplasts, meristematic cells, callus, pollen, leaves, anthers, roots, root tips, silk, flowers, kernels, ears, cobs, husks, or stalks.

Plant parts include harvestable parts and parts useful for propagation of progeny plants. Plant parts useful for propagation include, for example and without limitation: seed; fruit; a cutting; a seedling; a tuber; and a rootstock. A harvestable part of a plant may be any useful part of a plant, including, for example and without limitation: flower; pollen; seedling; tuber; leaf; stem; fruit; seed; and root.

A plant cell is the structural and physiological unit of the plant. Plant cells, as used herein, includes protoplasts and protoplasts with a cell wall. A plant cell may be in the form of an isolated single cell, or an aggregate of cells (e.g., a friable callus and a cultured cell), and may be part of a higher organized unit (e.g., a plant tissue, plant organ, and plant). Thus, a plant cell may be a protoplast, a gamete producing cell, or a cell or collection of cells that can regenerate into a whole plant. As such, a seed, which comprises multiple plant cells and is capable of regenerating into a whole plant, is considered a “plant part” in embodiments herein.

The term “protoplast”, as used herein, refers to a plant cell that had its cell wall completely or partially removed, with the lipid bilayer membrane thereof naked. Typically, a protoplast is an isolated plant cell without cell walls which has the potency for regeneration into cell culture or a whole plant.

As used herein the terms “native” or “natural” define a condition found in nature. A “native DNA sequence” is a DNA sequence present in nature that was produced by natural means or traditional breeding techniques but not generated by genetic engineering (e.g., using molecular biology/transformation techniques).

As used herein, “endogenous sequence” defines the native form of a polynucleotide, gene or polypeptide in its natural location in the organism or in the genome of an organism.

The term “isolated” as used herein means having been removed from its natural environment.

The term “purified”, as used herein relates to the isolation of a molecule or compound in a form that is substantially free of contaminants normally associated with the molecule or compound in a native or natural environment and means having been increased in purity as a result of being separated from other components of the original composition. The term “purified nucleic acid” is used herein to describe a nucleic acid sequence which has been separated from other compounds including, but not limited to polypeptides, lipids and carbohydrates.

The terms “polypeptide”, “peptide” and “protein” are used interchangeably to refer to a polymer of amino acid residues. The term also applies to amino acid polymers in which one or more amino acids are chemical analogues or modified derivatives of a corresponding naturally-occurring amino acids.

As used herein the terms “optimal maize genomic loci”, “optimal nongenic maize loci”, “optimal nongenic loci”, or “optimal genomic loci (OGL)” are used interchangeably to designate a native DNA sequence found in the nuclear genome of a maize plant that has the following properties: nongenic, hypomethylated, targetable, and in proximal location to a genic region, wherein the genomic region around the optimal maize genomic loci exemplifies evidence of recombination.

As used herein, the terms “nongenic maize sequence” or “nongenic maize genomic sequence” are used interchangeably to designate a native DNA sequence found in the nuclear genome of a maize plant, having a length of at least 1 Kb, and devoid of any open reading frames, gene sequences, or gene regulatory sequences. Furthermore, the nongenic maize sequence does not comprise any intron sequence (i.e., introns are excluded from the definition of nongenic). The nongenic sequence cannot be transcribed or translated into protein. Many plant genomes contain nongenic regions. As much as 95% of the genome can be nongenic, and these regions may be comprised of mainly repetitive DNA.

As used herein, a “genic region” is defined as a polynucleotide sequence that comprises an open reading frame encoding an RNA and/or polypeptide. The genic region may also encompass any identifiable adjacent 5′ and 3′ non-coding nucleotide sequences involved in the regulation of expression of the open reading frame up to about 2 Kb upstream of the coding region and 1 Kb downstream of the coding region, but possibly further upstream or downstream. A genic region further includes any introns that may be present in the genic region. Further, the genic region may comprise a single gene sequence, or multiple gene sequences interspersed with short spans (less than 1 Kb) of nongenic sequences.

As used herein a “nucleic acid of interest”, “DNA of interest”, or “donor” is defined as a nucleic acid/DNA sequence that has been selected for site directed, targeted insertion into the maize genome. A nucleic acid of interest can be of any length, for example between 2 and 50,000 nucleotides in length (or any integer value therebetween or thereabove), preferably between about 1,000 and 5,000 nucleotides in length (or any integer value therebetween). A nucleic acid of interest may comprise one or more gene expression cassettes that further comprise actively transcribed and/or translated gene sequences. Conversely, the nucleic acid of interest may comprise a polynucleotide sequence which does not comprise a functional gene expression cassette or an entire gene (e.g., may simply comprise regulatory sequences such as a promoter), or may not contain any identifiable gene expression elements or any actively transcribed gene sequence. The nucleic acid of interest may optionally contain an analytical domain. Upon insertion of the nucleic acid of interest into the maize genome, the inserted sequences are referred to as the “inserted DNA of interest”. Further, the nucleic acid of interest can be DNA or RNA, can be linear or circular, and can be single-stranded or double-stranded. It can be delivered to the cell as naked nucleic acid, as a complex with one or more delivery agents (e.g., liposomes, poloxamers, T-strand encapsulated with proteins, etc.) or contained in a bacterial or viral delivery vehicle, such as, for example, Agrobacterium tumefaciens or an adenovirus or an adeno-associated Virus (AAV), respectively.

As used herein the term “analytical domain” defines a nucleic acid sequence that contains functional elements that assist in the targeted insertion of nucleic acid sequences. For example, an analytical domain may contain specifically designed restriction enzyme sites, zinc finger binding sites, engineered landing pads or engineered transgene integration platforms and may or may not comprise gene regulatory elements or an open reading frame. See, for example, U.S. Patent Publication No 20110191899, incorporated herein by reference in its entirety.

As used herein the term “selected maize sequence” defines a native genomic DNA sequence of maize that has been chosen for analysis to determine if the sequence qualifies as an optimal nongenic maize genomic loci.

As used herein, the term “hypomethylation” or “hypomethylated”, in reference to a DNA sequence, defines a reduced state of methylated DNA nucleotide residues in a given sequence of DNA. Typically, the decreased methylation relates to the number of methylated adenine or cytosine residues, relative to the average level of methylation found in nongenic sequences present in the maize genome.

As used herein a “targetable sequence” is a polynucleotide sequence that is sufficiently unique in a nuclear genome to allow site specific, targeted insertion of a nucleic acid of interest into one specific sequence.

As used herein the term “non-repeating” sequence is defined as a sequence of at least 1 Kb in length that shares less than 40% identity to any other sequence within the Zea mays genome. Calculations of sequence identity can be determined using any standard technique known to those skilled in the art including, for example, scanning a selected maize sequence against the Zea mays c.v. B73 genome using a BLAST™ based homology search using the NCBI BLAST™ software (version 2.2.23) run using the default parameter settings (Stephen F. Altschul et al (1997), “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs”, Nucleic Acids Res. 25:3389-3402). For example, as the selected maize sequences (from the Zea mays c.v. B73 genome) were analyzed, the first BLAST™ hit identified from such a search represents the Zea mays c.v. B73 sequence itself. The second BLAST™ hit for each selected maize sequence was identified and the alignment coverage (represented as the percent of the selected maize sequence covered by the BLAST™ hit) of the hit was used as a measure of uniqueness of the selected maize sequence within the Zea mays genome. These alignment coverage values for the second BLAST™ hit ranged from a minimum of 0% to a maximum of 39.98% sequence identity. Any sequences that aligned at higher levels of sequence identity were not considered.

The term “in proximal location to a genic region” when used in reference to a nongenic sequence defines the relative location of the nongenic sequence to a genic region. Specifically, the number of genic regions within a 40 Kb neighborhood (i.e., within 40 Kb on either end of the selected optimal maize genomic loci sequence) is analyzed. This analysis was completed by assaying gene annotation information and the locations of known genes in the Zea mays genome were extracted from Maize Genome Database. For each of the 5,286 optimal nongenic maize genomic loci, a 40 Kb window around the optimal genomic loci sequence was defined and the number of annotated genes with locations overlapping this window was counted. The number of genic regions ranged from a minimum of 1 gene to a maximum of 9 genes within the 40 Kb neighborhood.

The term “known maize coding sequence” as used herein relates to any polynucleotide sequence identified from the Maize Genomic Database (available at www.maizegdb.org and Monaco, M., et al., Maize Metabolic Network Construction and Transcriptome Analysis. doi:10.3835/plantgenome2012.09.0025; Posted online 23 Jan. 2013) that comprise an open reading frame, either before or after processing of intron sequences, and are transcribed into mRNA and optionally translated into a protein sequence when placed under the control of the appropriate genetic regulatory elements. The known maize coding sequence can be a cDNA sequence or a genomic sequence. In some instances, the known maize coding sequence can be annotated as a functional protein. In other instances, the known maize coding sequence may not be annotated.

The term “predicted maize coding sequence” as used herein relates to any Expressed Sequence Tag (EST) polynucleotide sequences described in the Maize Genomic Database. ESTs are identified from cDNA libraries constructed using oligo(dT) primers to direct first-strand synthesis by reverse transcriptase. The resulting ESTs are single-pass sequencing reads of less than 500 bp obtained from either the 5′ or 3′ end of the cDNA insert. Multiple ESTs may be aligned into a single contig. The identified EST sequences are uploaded into the Maize Genomic Database, and can be searched via bioinformatics methods to predict corresponding genomic polynucleotide sequences that comprise a coding sequence that is transcribed into mRNA and optionally translated into a protein sequence when placed under the control of the appropriate genetic regulatory elements.

The term “evidence of recombination” as used herein relates to the meiotic recombination frequencies between any pair of Zea mays genomic markers across a chromosome region comprising the selected maize sequence. The recombination frequencies were calculated based on the ratio of the genetic distance between markers (in centimorgan (cM)) to the physical distance between the markers (in megabases (Mb)). For a selected maize sequence to have evidence of recombination, the selected maize sequence must contain at least one recombination event between two markers flanking the selected maize sequence as detected using a high resolution marker dataset generated from multiple mapping populations. (See for example, Jafar Mammadov, Wei Chen, Anastasia Chueva, Karthik Muthuraman, Ruihua Ren, David Meyer, and Siva Kumpatla. 2011. Distribution of Recombinant Frequencies across the Maize Genome. 52^(nd) Annual Maize Genetics Conference).

As used herein the term “relative location value” is a calculated value defining the distance of a genomic locus from its corresponding chromosomal centromere. For each selected maize sequence, the genomic distance from the native location of the selected maize sequence to the centromere of the chromosome that it is located on, is measured (in Bp). The relative location of selected maize sequence within the chromosome is represented as the ratio of its genomic distance to the centromere relative to the length of the specific chromosomal arm (measured in Bp) that it lies on. These relative location values for the optimal nongenic maize genomic loci dataset ranged from a minimum of 0.00373 to a maximum of 0.99908 ratio of genomic distance.

The term “exogenous DNA sequence” as used herein is any nucleic acid sequence that has been removed from its native location and inserted into a new location altering the sequences that flank the nucleic acid sequence that has been moved. For example, an exogenous DNA sequence may comprise a sequence from another species.

“Binding” refers to a sequence-specific, interaction between macromolecules (e.g., between a protein and a nucleic acid). Not all components of a binding interaction need be sequence-specific (e.g., contacts with phosphate residues in a DNA backbone), as long as the interaction as a whole is sequence-specific. Such interactions are generally characterized by a dissociation constant (Kd). “Affinity” refers to the strength of binding: increased binding affinity being correlated with a lower binding constant (Kd).

A “binding protein” is a protein that is able to bind to another molecule. A binding protein can bind to, for example, a DNA molecule (a DNA-binding protein), an RNA molecule (an RNA-binding protein) and/or a protein molecule (a protein-binding protein). In the case of a protein-binding protein, it can bind to itself (to form homodimers, homotrimers, etc.) and/or it can bind to one or more molecules of a different protein or proteins. A binding protein can have more than one type of binding activity. For example, zinc finger proteins have DNA-binding, RNA-binding and protein-binding activity.

As used herein the term “zinc fingers,” defines regions of amino acid sequence within a DNA binding protein binding domain whose structure is stabilized through coordination of a zinc ion.

A “zinc finger DNA binding protein” (or binding domain) is a protein, or a domain within a larger protein, that binds DNA in a sequence-specific manner through one or more zinc fingers, which are regions of amino acid sequence within the binding domain whose structure is stabilized through coordination of a zinc ion. The term zinc finger DNA binding protein is often abbreviated as zinc finger protein or ZFP. Zinc finger binding domains can be “engineered” to bind to a predetermined nucleotide sequence. Non-limiting examples of methods for engineering zinc finger proteins are design and selection. A designed zinc finger protein is a protein not occurring in nature whose design/composition results principally from rational criteria. Rational criteria for design include application of substitution rules and computerized algorithms for processing information in a database storing information of existing ZFP designs and binding data. See, for example, U.S. Pat. Nos. 6,140,081; 6,453,242; 6,534,261 and 6,794,136; see also WO 98/53058; WO 98/53059; WO 98/53060; WO 02/016536 and WO 03/016496.

A “TALE DNA binding domain” or “TALE” is a polypeptide comprising one or more TALE repeat domains/units. The repeat domains are involved in binding of the TALE to its cognate target DNA sequence. A single “repeat unit” (also referred to as a “repeat”) is typically 33-35 amino acids in length and exhibits at least some sequence homology with other TALE repeat sequences within a naturally occurring TALE protein. See, e.g., U.S. Patent Publication No. 20110301073, incorporated by reference herein in its entirety.

The CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas (CRISPR Associated) nuclease system. Briefly, a “CRISPR DNA binding domain” is a short stranded RNA molecule that acting in concert with the CAS enzyme can selectively recognize, bind, and cleave genomic DNA. The CRISPR/Cas system can be engineered to create a double-stranded break (DSB) at a desired target in a genome, and repair of the DSB can be influenced by the use of repair inhibitors to cause an increase in error prone repair. See, e.g., Jinek et al (2012) Science 337, p. 816-821, Jinek et al, (2013), eLife 2:e00471, and David Segal, (2013) eLife 2:e00563).

Zinc finger, CRISPR and TALE binding domains can be “engineered” to bind to a predetermined nucleotide sequence, for example via engineering (altering one or more amino acids) of the recognition helix region of a naturally occurring zinc finger. Similarly, TALEs can be “engineered” to bind to a predetermined nucleotide sequence, for example by engineering of the amino acids involved in DNA binding (the repeat variable diresidue or RVD region). Therefore, engineered DNA binding proteins (zinc fingers or TALEs) are proteins that are non-naturally occurring. Non-limiting examples of methods for engineering DNA-binding proteins are design and selection. A designed DNA binding protein is a protein not occurring in nature whose design/composition results principally from rational criteria. Rational criteria for design include application of substitution rules and computerized algorithms for processing information in a database storing information of existing ZFP and/or TALE designs and binding data. See, for example, U.S. Pat. Nos. 6,140,081; 6,453,242; and 6,534,261; see also WO 98/53058; WO 98/53059; WO 98/53060; WO 02/016536 and WO 03/016496 and U.S. Publication Nos. 20110301073, 20110239315 and 20119145940.

A “selected” zinc finger protein, CRISPR or TALE is a protein not found in nature whose production results primarily from an empirical process such as phage display, interaction trap or hybrid selection. See e.g., U.S. Pat. Nos. 5,789,538; 5,925,523; 6,007,988; 6,013,453; 6,200,759; WO 95/19431; WO 96/06166; WO 98/53057; WO 98/54311; WO 00/27878; WO 01/60970 WO 01/88197 and WO 02/099084 and U.S. Publication Nos. 20110301073, 20110239315 and 20119145940.

“Recombination” refers to a process of exchange of genetic information between two polynucleotides, including but not limited to, donor capture by non-homologous end joining (NHEJ) and homologous recombination. For the purposes of this disclosure, “homologous recombination (HR)” refers to the specialized form of such exchange that takes place, for example, during repair of double-strand breaks in cells via homology-directed repair mechanisms. This process requires nucleotide sequence homology, uses a “donor” molecule to template repair of a “target” molecule (i.e., the nucleotide sequence that experienced the double-strand break), and is variously known as “non-crossover gene conversion” or “short tract gene conversion,” because it leads to the transfer of genetic information from the donor to the target. Without wishing to be bound by any particular theory, such transfer can involve mismatch correction of heteroduplex DNA that forms between the broken target and the donor, and/or “synthesis-dependent strand annealing,” in which the donor is used to resynthesize genetic information that will become part of the target, and/or related processes. Such specialized HR often results in an alteration of the sequence of the target molecule such that part or all of the sequence of the donor polynucleotide is incorporated into the target polynucleotide. For HR-directed integration, the donor molecule contains at least 2 regions of homology to the genome (“homology arms”) of least 50-100 base pairs in length. See, e.g., U.S. Patent Publication No. 20110281361.

In the methods of the disclosure, one or more targeted nucleases as described herein create a double-stranded break in the target sequence (e.g., cellular chromatin) at a predetermined site, and a “donor” polynucleotide, having homology to the nucleotide sequence in the region of the break for HR mediated integration or having no homology to the nucleotide sequence in the region of the break for NHEJ mediated integration, can be introduced into the cell. The presence of the double-stranded break has been shown to facilitate integration of the donor sequence. The donor sequence may be physically integrated or, alternatively, the donor polynucleotide is used as a template for repair of the break via homologous recombination, resulting in the introduction of all or part of the nucleotide sequence as in the donor into the cellular chromatin. Thus, a first sequence in cellular chromatin can be altered and, in certain embodiments, can be converted into a sequence present in a donor polynucleotide. Thus, the use of the terms “replace” or “replacement” can be understood to represent replacement of one nucleotide sequence by another, (i.e., replacement of a sequence in the informational sense), and does not necessarily require physical or chemical replacement of one polynucleotide by another. In any of the methods described herein, additional pairs of zinc-finger proteins, CRISPRS or TALEN can be used for additional double-stranded cleavage of additional target sites within the cell.

Any of the methods described herein can be used for insertion of a donor of any size and/or partial or complete inactivation of one or more target sequences in a cell by targeted integration of donor sequence that disrupts expression of the gene(s) of interest. Cell lines with partially or completely inactivated genes are also provided.

Furthermore, the methods of targeted integration as described herein can also be used to integrate one or more exogenous sequences. The exogenous nucleic acid sequence can comprise, for example, one or more genes or cDNA molecules, or any type of coding or noncoding sequence, as well as one or more control elements (e.g., promoters). In addition, the exogenous nucleic acid sequence (transgene) may produce one or more RNA molecules (e.g., small hairpin RNAs (shRNAs), inhibitory RNAs (RNAis), microRNAs (miRNAs), etc.), or protein.

“Cleavage” as used herein defines the breakage of the phosphate-sugar backbone of a DNA molecule. Cleavage can be initiated by a variety of methods including, but not limited to, enzymatic or chemical hydrolysis of a phosphodiester bond. Both single-stranded cleavage and double-stranded cleavage are possible, and double-stranded cleavage can occur as a result of two distinct single-stranded cleavage events. DNA cleavage can result in the production of either blunt ends or staggered ends. In certain embodiments, fusion polypeptides are used for targeted double-stranded DNA cleavage. A “cleavage domain” comprises one or more polypeptide sequences which possesses catalytic activity for DNA cleavage. A cleavage domain can be contained in a single polypeptide chain or cleavage activity can result from the association of two (or more) polypeptides.

A “cleavage half-domain” is a polypeptide sequence which, in conjunction with a second polypeptide (either identical or different) forms a complex having cleavage activity (preferably double-strand cleavage activity). The terms “first and second cleavage half-domains;” “+ and − cleavage half-domains” and “right and left cleavage half-domains” are used interchangeably to refer to pairs of cleavage half-domains that dimerize.

An “engineered cleavage half-domain” is a cleavage half-domain that has been modified so as to form obligate heterodimers with another cleavage half-domain (e.g., another engineered cleavage half-domain). See, also, U.S. Patent Publication Nos. 2005/0064474, 20070218528, 2008/0131962 and 2011/0201055, incorporated herein by reference in their entireties.

A “target site” or “target sequence” refers to a portion of a nucleic acid to which a binding molecule will bind, provided sufficient conditions for binding exist.

Nucleic acids include DNA and RNA, can be single- or double-stranded; can be linear, branched or circular; and can be of any length. Nucleic acids include those capable of forming duplexes, as well as triplex-forming nucleic acids. See, for example, U.S. Pat. Nos. 5,176,996 and 5,422,251. Proteins include, but are not limited to, DNA-binding proteins, transcription factors, chromatin remodeling factors, methylated DNA binding proteins, polymerases, methylases, demethylases, acetylases, deacetylases, kinases, phosphatases, integrases, recombinases, ligases, topoisomerases, gyrases and helicases.

A “product of an exogenous nucleic acid” includes both polynucleotide and polypeptide products, for example, transcription products (polynucleotides such as RNA) and translation products (polypeptides).

A “fusion” molecule is a molecule in which two or more subunit molecules are linked, for example, covalently. The subunit molecules can be the same chemical type of molecule, or can be different chemical types of molecules. Examples of the first type of fusion molecule include, but are not limited to, fusion proteins (for example, a fusion between a ZFP DNA-binding domain and a cleavage domain) and fusion nucleic acids (for example, a nucleic acid encoding the fusion protein described supra). Examples of the second type of fusion molecule include, but are not limited to, a fusion between a triplex-forming nucleic acid and a polypeptide, and a fusion between a minor groove binder and a nucleic acid. Expression of a fusion protein in a cell can result from delivery of the fusion protein to the cell or by delivery of a polynucleotide encoding the fusion protein to a cell, wherein the polynucleotide is transcribed, and the transcript is translated, to generate the fusion protein. Trans-splicing, polypeptide cleavage and polypeptide ligation can also be involved in expression of a protein in a cell. Methods for polynucleotide and polypeptide delivery to cells are presented elsewhere in this disclosure.

For the purposes of the present disclosure, a “gene”, includes a DNA region encoding a gene product (see infra), as well as all DNA regions which regulate the production of the gene product, whether or not such regulatory sequences are adjacent or operably linked to coding and/or transcribed sequences. Accordingly, a gene includes, but is not necessarily limited to, promoter sequences, terminators, translational regulatory sequences such as ribosome binding sites and internal ribosome entry sites, enhancers, silencers, insulators, boundary elements, replication origins, matrix attachment sites and locus control regions.

“Gene expression” refers to the conversion of the information, contained in a gene, into a gene product. A gene product can be the direct transcriptional product of a gene (e.g., mRNA, tRNA, rRNA, antisense RNA, interfering RNA, ribozyme, structural RNA or any other type of RNA) or a protein produced by translation of a mRNA. Gene products also include RNAs which are modified, by processes such as capping, polyadenylation, methylation, and editing, and proteins modified by, for example, methylation, acetylation, phosphorylation, ubiquitination, ADP-ribosylation, myristilation, and glycosylation.

Sequence identity: The term “sequence identity” or “identity,” as used herein in the context of two nucleic acid or polypeptide sequences, refers to the residues in the two sequences that are the same when aligned for maximum correspondence over a specified comparison window.

As used herein, the term “percentage of sequence identity” refers to the value determined by comparing two optimally aligned sequences (e.g., nucleic acid sequences, and amino acid sequences) over a comparison window, wherein the portion of the sequence in the comparison window may comprise additions or deletions (i.e., gaps) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical nucleotide or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the comparison window, and multiplying the result by 100 to yield the percentage of sequence identity.

Methods for aligning sequences for comparison are well-known in the art. Various programs and alignment algorithms are described in, for example: Smith and Waterman (1981) Adv. Appl. Math. 2:482; Needleman and Wunsch (1970) J. Mol. Biol. 48:443; Pearson and Lipman (1988) Proc. Natl. Acad. Sci. U.S.A. 85:2444; Higgins and Sharp (1988) Gene 73:237-44; Higgins and Sharp (1989) CABIOS 5:151-3; Corpet et al. (1988) Nucleic Acids Res. 16:10881-90; Huang et al. (1992) Comp. Appl. Biosci. 8:155-65; Pearson et al. (1994) Methods Mol. Biol. 24:307-31; Tatiana et al. (1999) FEMS Microbiol. Lett. 174:247-50. A detailed consideration of sequence alignment methods and homology calculations can be found in, e.g., Altschul et al. (1990) J. Mol. Biol. 215:403-10. The National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool (BLAST™; Altschul et al. (1990)) is available from several sources, including the National Center for Biotechnology Information (Bethesda, Md.), and on the internet, for use in connection with several sequence analysis programs. A description of how to determine sequence identity using this program is available on the internet under the “help” section for BLAST™. For comparisons of nucleic acid sequences, the “Blast 2 sequences” function of the BLAST™ (Blastn) program may be employed using the default parameters. Nucleic acid sequences with even greater similarity to the reference sequences will show increasing percentage identity when assessed by this method.

Specifically hybridizable/Specifically complementary: As used herein, the terms “specifically hybridizable” and “specifically complementary” are terms that indicate a sufficient degree of complementarity, such that stable and specific binding occurs between the nucleic acid molecule and a target nucleic acid molecule. Hybridization between two nucleic acid molecules involves the formation of an anti-parallel alignment between the nucleic acid sequences of the two nucleic acid molecules. The two molecules are then able to form hydrogen bonds with corresponding bases on the opposite strand to form a duplex molecule that, if it is sufficiently stable, is detectable using methods well known in the art. A nucleic acid molecule need not be 100% complementary to its target sequence to be specifically hybridizable. However, the amount of sequence complementarity that must exist for hybridization to be specific is a function of the hybridization conditions used.

Hybridization conditions resulting in particular degrees of stringency will vary depending upon the nature of the hybridization method of choice and the composition and length of the hybridizing nucleic acid sequences. Generally, the temperature of hybridization and the ionic strength (especially the Na+ and/or Mg++ concentration) of the hybridization buffer will determine the stringency of hybridization, though wash times also influence stringency. Calculations regarding hybridization conditions required for attaining particular degrees of stringency are known to those of ordinary skill in the art, and are discussed, for example, in Sambrook et al. (ed.) Molecular Cloning: A Laboratory Manual, 2nd ed., vol. 1-3, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989, chapters 9 and 11; and Hames and Higgins (eds.) Nucleic Acid Hybridization, IRL Press, Oxford, 1985. Further detailed instruction and guidance with regard to the hybridization of nucleic acids may be found, for example, in Tijssen, “Overview of principles of hybridization and the strategy of nucleic acid probe assays,” in Laboratory Techniques in Biochemistry and Molecular Biology-Hybridization with Nucleic Acid Probes, Part I, Chapter 2, Elsevier, N Y, 1993; and Ausubel et al., Eds., Current Protocols in Molecular Biology, Chapter 2, Greene Publishing and Wiley-Interscience, N Y, 1995.

As used herein, “stringent conditions” encompass conditions under which hybridization will only occur if there is less than 20% mismatch between the hybridization molecule and a sequence within the target nucleic acid molecule. “Stringent conditions” include further particular levels of stringency. Thus, as used herein, “moderate stringency” conditions are those under which molecules with more than 20% sequence mismatch will not hybridize; conditions of “high stringency” are those under which sequences with more than 10% mismatch will not hybridize; and conditions of “very high stringency” are those under which sequences with more than 5% mismatch will not hybridize. The following are representative, non-limiting hybridization conditions.

High Stringency condition (detects sequences that share at least 90% sequence identity): Hybridization in 5×SSC buffer (wherein the SSC buffer contains a detergent such as SDS, and additional reagents like salmon sperm DNA, EDTA, etc.) at 65° C. for 16 hours; wash twice in 2×SSC buffer (wherein the SSC buffer contains a detergent such as SDS, and additional reagents like salmon sperm DNA, EDTA, etc.) at room temperature for 15 minutes each; and wash twice in 0.5×SSC buffer (wherein the SSC buffer contains a detergent such as SDS, and additional reagents like salmon sperm DNA, EDTA, etc.) at 65° C. for 20 minutes each.

Moderate Stringency condition (detects sequences that share at least 80% sequence identity): Hybridization in 5×-6×SSC buffer (wherein the SSC buffer contains a detergent such as SDS, and additional reagents like salmon sperm DNA, EDTA, etc.) at 65-70° C. for 16-20 hours; wash twice in 2×SSC buffer (wherein the SSC buffer contains a detergent such as SDS, and additional reagents like salmon sperm DNA, EDTA, etc.) at room temperature for 5-20 minutes each; and wash twice in 1×SSC buffer (wherein the SSC buffer contains a detergent such as SDS, and additional reagents like salmon sperm DNA, EDTA, etc.) at 55-70° C. for 30 minutes each.

Non-stringent control condition (sequences that share at least 50% sequence identity will hybridize): Hybridization in 6×SSC buffer (wherein the SSC buffer contains a detergent such as SDS, and additional reagents like salmon sperm DNA, EDTA, etc.) at room temperature to 55° C. for 16-20 hours; wash at least twice in 2×-3×SSC buffer (wherein the SSC buffer contains a detergent such as SDS, and additional reagents like salmon sperm DNA, EDTA, etc.) at room temperature to 55° C. for 20-30 minutes each.

As used herein, the term “substantially homologous” or “substantial homology,” with regard to a contiguous nucleic acid sequence, refers to contiguous nucleotide sequences that hybridize under stringent conditions to the reference nucleic acid sequence. For example, nucleic acid sequences that are substantially homologous to a reference nucleic acid sequence are those nucleic acid sequences that hybridize under stringent conditions (e.g., the Moderate Stringency conditions set forth, supra) to the reference nucleic acid sequence. Substantially homologous sequences may have at least 80% sequence identity. For example, substantially homologous sequences may have from about 80% to 100% sequence identity, such as about 81%; about 82%; about 83%; about 84%; about 85%; about 86%; about 87%; about 88%; about 89%; about 90%; about 91%; about 92%; about 93%; about 94% about 95%; about 96%; about 97%; about 98%; about 98.5%; about 99%; about 99.5%; and about 100%. The property of substantial homology is closely related to specific hybridization. For example, a nucleic acid molecule is specifically hybridizable when there is a sufficient degree of complementarity to avoid non-specific binding of the nucleic acid to non-target sequences under conditions where specific binding is desired, for example, under stringent hybridization conditions.

In some instances “homologous” may be used to refer to the relationship of a first gene to a second gene by descent from a common ancestral DNA sequence. In such instances, the term, homolog, indicates a relationship between genes separated by the event of speciation (see ortholog) or to the relationship between genes separated by the event of genetic duplication (see paralog). In other instances “homologous” may be used to refer to the level of sequence identity between one or more polynucleotide sequences, in such instances the one or more polynucleotide sequences do not necessarily descend from a common ancestral DNA sequence. Those with skill in the art are aware of the interchangeably of the term “homologous” and appreciate the proper application of the term.

As used herein, the term “ortholog” (or “orthologous”) refers to a gene in two or more species that has evolved from a common ancestral nucleotide sequence, and may retain the same function in the two or more species.

As used herein, the term “paralogous” refers to genes related by duplication within a genome. Orthologs retain the same function in the course of evolution, whereas paralogs evolve new functions, even if these new functions are unrelated to the original gene function.

As used herein, two nucleic acid sequence molecules are said to exhibit “complete complementarity” when every nucleotide of a sequence read in the 5′ to 3′ direction is complementary to every nucleotide of the other sequence when read in the 3′ to 5′ direction. A nucleotide sequence that is complementary to a reference nucleotide sequence will exhibit a sequence identical to the reverse complement sequence of the reference nucleotide sequence. These terms and descriptions are well defined in the art and are easily understood by those of ordinary skill in the art.

When determining the percentage of sequence identity between amino acid sequences, it is well-known by those of skill in the art that the identity of the amino acid in a given position provided by an alignment may differ without affecting desired properties of the polypeptides comprising the aligned sequences. In these instances, the percent sequence identity may be adjusted to account for similarity between conservatively substituted amino acids. These adjustments are well-known and commonly used by those of skill in the art. See, e.g., Myers and Miller (1988) Computer Applications in Biosciences 4:11-7. Statistical methods are known in the art and can be used in analysis of the identified 5,286 optimal genomic loci.

As an embodiment, the identified optimal genomic loci comprising 5,286 individual optimal genomic loci sequences can be analyzed via an F-distribution test. In probability theory and statistics, the F-distribution is a continuous probability distribution. The F-distribution test is a statistical significance test that has an F-distribution, and is used when comparing statistical models that have been fit to a data set, to identify the best-fitting model. An F-distribution is a continuous probability distribution, and is also known as Snedecor's F-distribution or the Fisher-Snedecor distribution. The F-distribution arises frequently as the null distribution of a test statistic, most notably in the analysis of variance. The F-distribution is a right-skewed distribution. The F-distribution is an asymmetric distribution that has a minimum value of 0, but no maximum value. The curve reaches a peak not far to the right of 0, and then gradually approaches the horizontal axis the larger the F value is. The F-distribution approaches, but never quite touches the horizontal axis. It will be appreciated that in other embodiments, variations on this equation, or indeed different equations, may be derived and used by the skilled person and are applicable to the analysis of 5,286 individual optimal genomic loci sequences.

Operably linked: A first nucleotide sequence is “operably linked” with a second nucleotide sequence when the first nucleotide sequence is in a functional relationship with the second nucleotide sequence. For instance, a promoter is operably linked to a coding sequence if the promoter affects the transcription or expression of the coding sequence. When recombinantly produced, operably linked nucleotide sequences are generally contiguous and, where necessary to join two protein-coding regions, in the same reading frame. However, nucleotide sequences need not be contiguous to be operably linked.

The term, “operably linked,” when used in reference to a regulatory sequence and a coding sequence, means that the regulatory sequence affects the expression of the linked coding sequence. “Regulatory sequences,” “regulatory elements”, or “control elements,” refer to nucleotide sequences that influence the timing and level/amount of transcription, RNA processing or stability, or translation of the associated coding sequence. Regulatory sequences may include promoters; translation leader sequences; introns; enhancers; stem-loop structures; repressor binding sequences; termination sequences; polyadenylation recognition sequences; etc. Particular regulatory sequences may be located upstream and/or downstream of a coding sequence operably linked thereto. Also, particular regulatory sequences operably linked to a coding sequence may be located on the associated complementary strand of a double-stranded nucleic acid molecule.

When used in reference to two or more amino acid sequences, the term “operably linked” means that the first amino acid sequence is in a functional relationship with at least one of the additional amino acid sequences.

The disclosed methods and compositions include fusion proteins comprising a cleavage domain operably linked to a DNA-binding domain (e.g., a ZFP) in which the DNA-binding domain by binding to a sequence in the Zea mays optimal genomic locus directs the activity of the cleavage domain to the vicinity of the sequence and, hence, induces a double stranded break in the optimal genomic locus. As set forth elsewhere in this disclosure, a zinc finger domain can be engineered to bind to virtually any desired sequence. Accordingly, one or more DNA-binding domains can be engineered to bind to one or more sequences in the optimal genomic locus. Expression of a fusion protein comprising a DNA-binding domain and a cleavage domain in a cell, effects cleavage at or near the target site.

EMBODIMENTS

Targeting transgenes and transgene stacks to specific locations in the Zea mays genome will improve the quality of transgenic events, reduce costs associated with production of transgenic events and provide new methods for making transgenic plant products such as sequential gene stacking. Overall, targeting transgenes to specific genomic sites is likely to be commercially beneficial. Significant advances have been made in the last few years towards development of site-specific nucleases such as ZFNs, CRISPRs, and TALENs that can facilitate addition of donor polynucleotides to pre-selected sites in plant and other genomes. However, much less is known about the attributes of genomic sites that are suitable for targeting. Historically, non-essential genes and pathogen (viral) integration sites in genomes have been used as loci for targeting. The number of such sites in genomes is rather limiting and there is therefore a need for identification and characterization of optimal genomic loci that can be used for targeting of donor polynucleotide sequences. In addition to being amenable to targeting, optimal genomic loci are expected to be neutral sites that can support transgene expression and breeding applications.

Applicants have recognized that additional criteria are desirable for insertion sites and have combined these criteria to identify and select optimal sites in the maize genome for the insertion of exogenous sequences. For targeting purposes, the site of selected insertion needs to be unique and in a non-repetitive region of the Zea mays genome. Likewise, the optimal genomic site for insertion should possess minimal undesirable phenotypic effects and be susceptible to recombination events to facilitate introgression into agronomically elite lines using traditional breeding techniques. In order to identify the genomic loci that meet the listed criteria, the Zea mays genome was scanned using a customized bioinformatics approach and genome scale datasets to identify novel genomic loci possessing characteristics that are beneficial for the integration of polynucleotide donor sequence and the subsequent expression of a inserted coding sequence.

I. Identification of Nongenic Maize Genomic Loci

In accordance with one embodiment a method is provided for identifying optimal nongenic maize genomic sequence for insertion of exogenous sequences. The method comprises the steps of first identifying maize genomic sequences of at least 1 Kb in length that are hypomethylated. In one embodiment the hypomethylated genomic sequence is 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 5.5, 6, 6.5, 7, 7.5, 8, 8.5, 9, 10, 11, 12, 13, 14, 15, 16 or 17 Kb in length. In one embodiment the hypomethylated genomic sequence is about 1 to about 4 Kb in length and in a further embodiment is about 2 Kb in length. A sequence is considered hypomethylated if it has less than 1% DNA methylation within the sequence. In one embodiment the methylation status is measured based on the presence of 5-methylcytosine at one or more CpG dinucleotides, CHG or CHH trinucleotides within a selected maize sequence, relative to the amount of total cytosines found at corresponding CpG dinucleotides, CHG or CHH trinucleotides within a normal control DNA sample. CHH methylation indicates a 5-methylcytosine followed by two nucleotides that many not be guanine and CHG methylation refers to a 5-methylcytosine preceding an adenine, thymine or cytosine based followed by guanine. More particularly, in one embodiment the selected maize sequence has less than 1, 2 or 3 methylated nucleotides per 500 nucleotides of the selected maize sequence. In one embodiment the selected maize sequence has less than one, two, or three 5-methylcytosines at CpG dinucleotides per 500 nucleotides of the selected maize sequence. In one embodiment the selected maize sequence is 1 to 4 Kb in length and comprises a 1 Kb sequence devoid of 5-methylcytosines. In one embodiment the selected maize sequence is 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 5.5, 6, 6.5, 7, 7.5, 8, or 8.5 Kb in length and contains 1 or 0 methylated nucleotides in its entire length. In one embodiment the selected maize sequence is 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 5.5, 6, 6.5, 7, 7.5, 8, or 8.5 Kb in length and contains no 5-methylcytosines at CpG dinucleotides within in its entire length. In accordance with one embodiment the methylation of a selected maize sequence may vary based on source tissue. In such embodiments the methylation levels used to determine if a sequence is hypomethylated represents the average amount of methylation in the sequences isolated from two or more tissues (e.g., from root and shoot).

In addition to the requirement that an optimal genomic site be hypomethylated, the selected maize sequence must also be nongenic. Accordingly, all hypomethylated genomic sequences are further screened to eliminate hypomethylated sequences that contain a genic region. This includes any open reading frames regardless of whether the transcript encodes a protein. Hypomethylated genomic sequences that include genic regions, including any identifiable adjacent 5′ and 3′ non-coding nucleotide sequences involved in the regulation of expression of an open reading frame and any introns that may be present in the genic region, are excluded from the optimal nongenic maize genomic locus of the present disclosure.

Optimal nongenic maize genomic loci must also be sequences that have demonstrated evidence of recombination. In one embodiment the selected maize sequence must be one where at least one recombination event has been detected between two markers flanking the selected maize sequence as detected using a high resolution marker dataset generated from multiple mapping populations. In one embodiment the pair of markers flanking a 0.5, 1, 1.5 Mb maize genomic sequence comprising the selected maize sequence are used to calculate the recombinant frequency for the selected maize sequence. Recombination frequencies between each pairs of markers (measured in centimorgan (cM)) to the genomic physical distance between the markers (in Mb)) must be greater than 0 cM/Mb. In one embodiment the recombination frequency for a 1 Mb maize genomic sequence comprising the selected maize sequence ranges from about 0.00041 to about 4.0. In one embodiment the recombination frequency for a 1 Mb maize genomic sequence comprising the selected maize sequence ranges from about 0.5 to about 5.0. In one embodiment an optimal genomic loci is one where recombination events have been detected within the selected maize sequence.

An optimal nongenic maize genomic loci will also be a targetable sequence, i.e., a sequence that is relatively unique in the maize genome such that a gene targeted to the selected maize sequence will only insert in one location of the maize genome. In one embodiment the entire length of the optimal genomic sequence shares less than 30%, 35%, or 40%, sequence identity with another sequence of similar length contained in the maize genome. Accordingly in one embodiment the selected maize sequence cannot comprise a 1 Kb sequence that shares more than 25%, 30%, 35%, or 40% sequence identity with another 1 Kb sequence contained in the maize genome. In a further embodiment the selected maize sequence cannot comprise a 500 bp sequence that shares more than 30%, 35%, or 40% sequence identity with another 500 bp sequence contained in the maize genome. In one embodiment the selected maize sequence cannot comprise a 1 KB sequence that shares more than 40% sequence identity with another 1 Kb sequence contained in the maize genome.

An optimal nongenic maize genomic loci will also be proximal to a genic region. More particularly, a selected maize sequence must be located in the vicinity of a genic region (e.g., a genic region must be located within 40 Kb of genomic sequence flanking and contiguous with either end of the selected maize as found in the native genome). In one embodiment a genic region is located within 10, 20, 30 or 40 Kb of contiguous genomic sequence located at either end of the selected maize sequence as found in the native maize genome. In one embodiment two or more genic regions are located within 10, 20, 30 or 40 Kb of contiguous genomic sequence flanking the two ends of the selected maize sequence. In one embodiment 1-9 genic regions are located within 10, 20, 30 or 40 Kb of contiguous genomic sequence flanking the two ends of the selected maize sequence. In one embodiment two or more genic regions are located within a 20, 30 or 40 Kb genomic sequence comprising the selected maize sequence. In one embodiment 1-9 genic regions are located within a 40 Kb genomic sequence comprising the selected maize sequence. In one embodiment the genic region located within a 10, 20, 30 or 40 Kb of contiguous genomic sequence flanking the selected maize sequence comprises a known gene in the Zea mays genome.

In accordance with one embodiment a modified nongenic maize genomic loci is provided wherein the loci is at least 1 KB in length, is nongenic, comprises no methylated cytosine residues, has a recombination frequency of greater than 0.00041 cM/Mb over a 1 Mb genomic region encompassing the maize genomic loci and a 1 Kb sequence of the maize genomic loci shares less than 40% sequence identity with any other 1 Kb sequence contained in the maize genome, wherein the nongenic maize genomic loci is modified by the insertion of a DNA of interest into the nongenic maize genomic loci.

In accordance with one embodiment a method for identifying optimal nongenic maize genomic loci is provided. In some embodiments, the method first comprises screening the maize genome to create a first pool of selected maize sequences that have a minimal length of 1 Kb and are hypomethylated, optionally wherein the genomic sequence has less than 1% methylation or wherein the genomic sequence is devoid of any methylated cytosine residues. This first pool of selected maize sequences can be further screened to eliminate loci that do not meet the requirements for optimal nongenic maize genomic loci. Maize genomic sequences that encode maize transcripts, share greater than 40% or higher sequence identity with another sequence of similar length, do not exhibit evidence of recombination, and do not have a known open reading frame within 40 Kb of the selected maize sequence, are eliminated from the first pool of sequences, leaving a second pool of sequences that qualify as optimal nongenic maize loci. In one embodiment any selected maize sequences that do not have a known maize gene, or a sequence comprising a 2 Kb upstream and/or 1 Kb downstream region of a known maize gene, within 40 Kb of one end of said nongenic sequence are eliminated from the first pool of sequences. In one embodiment any selected maize sequences that do not contain a known gene that expresses a protein within 40 Kb of the selected maize sequence are eliminated. In one embodiment any selected maize sequences that do not have a recombination frequency of greater than 0.00041 cM/Mb are eliminated.

Using these selection criteria applicants have identified select optimal genomic loci of Zea mays that serve as optimal nongenic maize genomic loci, the sequences of which are disclosed as SEQ ID NO: 1-SEQ ID NO: 5,286. The present disclosure also encompasses natural variants or modified derivatives of the identified optimal nongenic maize genomic loci wherein the variant or derivative loci comprise a sequence that differs from any sequence of SEQ ID NO: 1-SEQ ID NO: 5,286 by 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 nucleotides. In one embodiment optimal nongenic maize genomic loci for use in accordance with the present disclosure comprise sequences selected from SEQ ID NO: 1-SEQ ID NO: 5,286 or sequences that share 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity with a sequence selected from SEQ ID NO: 1-SEQ ID NO: 5,286.

In another embodiment, optimal nongenic maize genomic loci for use in accordance with the present disclosure comprise sequences selected from any variety of maize or corn plants. In a further embodiment optimal nongenic maize genomic loci for use in accordance with the present disclosure comprise sequences selected from yellow corn inbreds. Accordingly, a yellow corn inbred includes dent or flint yellow corn inbred plants, including agronomically elite varieties thereof. In a subsequent embodiment, optimal nongenic maize genomic loci for use in accordance with the present disclosure comprise sequences selected from transformable corn lines. In an embodiment, representative transformable corn lines include; Hi-II, B73, B104, Mo 17, W22, A188, H99, and derivatives thereof. One of skill in the art will appreciate that as a result of phylogenetic divergence, various types of corn lines do not contain identical genomic DNA sequences, and that polymorphisms or allelic variation may be present within genomic sequences. In an embodiment, the present disclosure encompasses such polymorphism or allelic variations of the identified optimal nongenic maize genomic loci wherein the polymorphisms or allelic variation comprise a sequence that differs from any sequence of SEQ ID NO: 1-SEQ ID NO: 5,286 by 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 nucleotides. In a further embodiment, the present disclosure encompasses such polymorphisms or allelic variations of the identified optimal nongenic maize genomic loci wherein the polymorphisms or allelic variations comprise a sequence that shares 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity with any sequence of SEQ ID NO: 1-SEQ ID NO: 5,286.

The identified optimal genomic loci comprising 5,286 individual sequences can be categorized into various subgroupings by further analysis using a multivariate analysis method. Application of any multivariate analysis statistical programs is used to uncover the latent structure (dimensions) of a set of variables. A number of different types of multivariate algorithms can be used, for example the data set can be analyzed using multiple regression analysis, logistic regression analysis, discriminate analysis, multivariate analysis of variance (MANOVA), factor analysis (including both common factor analysis, and principal component analysis), cluster analysis, multidimensional scaling, correspondence analysis, conjoint analysis, canonical analysis, canonical correlation, and structural equation modeling.

In accordance with one embodiment the optimal nongenic maize genomic loci are further analyzed using multivariate data analysis such as Principal Component Analysis (PCA). Only a brief description will be given here, more information can be found in H. Martens, T. Naes, Multivariate Calibration, Wiley, N.Y., 1989. PCA evaluates the underlying dimensionality (latent variables) of the data, and gives an overview of the dominant patterns and major trends in the data. In one embodiment, the optimal nongenic maize genomic loci can be sorted into clusters via a principal component analysis (PCA) statistical method. The PCA is a mathematical procedure that uses an orthogonal transformation to convert a set of observations of possibly correlated variables into a set of values of linearly uncorrelated variables called principal components. The number of principal components is less than or equal to the number of original variables. This transformation is defined in such a way that the first principal component has the largest possible variance (that is, accounts for as much of the variability in the data as possible), and each succeeding component in turn has the highest variance possible under the constraint that it be orthogonal to (i.e., uncorrelated with) the preceding components. Principal components are guaranteed to be independent if the data set is jointly normally distributed. PCA is sensitive to the relative scaling of the original variables. Examples of the use of PCA to cluster a set of entities based on features of the entities include; Ciampitti, I. et al., (2012) Crop Science, 52(6); 2728-2742, Chemometrics: A Practical Guide, Kenneth R. Beebe, Randy J. Pell, and Mary Beth Seasholtz, Wiley-Interscience, 1 edition, 1998, U.S. Pat. No. 8,385,662, and European Patent No. 2,340,975.

In accordance with one embodiment a principal component analysis (PCA) was conducted on the 5,286 optimal maize genomic loci using the following 10 features for each identified optimal maize genomic loci:

1. Length of the hypo-methylated region around the optimal genomic loci (OGL)

-   -   a. Genome wide methylation profiles for root and shoot tissues         were established using Illumina/Solexa 1G parallel sequencing         data after digesting genomic DNA with a methylation-sensitive         restriction enzyme (Wang et al., (2009) Genome-Wide and         Organ-Specific Landscapes of Epigenetic Modifications and Their         Relationships to mRNA and Small RNA Transcriptomes in Maize.         Plant Cell 21(4): 1053-1069). Sequences mapping to the genome         indicated the presence of DNA methylation at the mapped         locations and chromosomal stretches without mapped sequences         indicated an absence of methylation (hypo-methylation). The         length of the hypo-methylated region around each of the OGLs was         calculated using the described methylation profiles.

2. Rate of Recombination in a 1 MB region around the OGL

-   -   a. For each OGL, a pair of markers on either side of the OGL,         within a 1 Mb window, was identified. Recombination frequencies         between each pairs of markers across the chromosome were         calculated based on the ratio of the genetic distance between         markers (in centimorgan (cM)) to the genomic physical distance         between the markers (in Mb).

3. Level of OGL sequence uniqueness

-   -   a. For each OGL, the nucleotide sequence of the OGL was scanned         against the Zea mays c.v. B73 genome using a BLAST based         homology search. As these OGL sequences are identified from the         Zea mays c.v. B73 genome, the first BLAST hit identified through         this search represents the OGL sequence itself. The second BLAST         hit for each OGL was identified and the alignment coverage of         the hit was used as a measure of uniqueness of the OGL sequence         within the Zea mays genome.

4. Distance from the OGL to the closest gene in its neighborhood

-   -   a. Gene annotation information and the location of known genes         in the Zea mays c.v. B73 genome were extracted from Maize Genome         DB (www.maizegdb.org). For each OGL, the closest annotated gene         in its upstream or downstream neighborhood was identified and         the distance between the OGL sequence and the gene was measured         (in bp).

5. GC % in the OGLneighborhood

-   -   a. For each OGL, the nucleotide sequence was analyzed to         estimate the number of Guanine and Cytosine bases present. This         count was represented as a percentage of the sequence length of         each OGLand provides a measure for GC %.

6. Number of genes in a 40 Kb neighborhood around the OGL

-   -   a. Gene annotation information and the location of known genes         in the Zea mays c.v. B73 genome were extracted from Maize Genome         DB (www.maizegdb.org). For each OGL, a 40 Kb window around the         OGL was defined and the number of annotated genes with locations         overlapping this window was counted.

7. Average gene expression in a 40 Kb neighborhood around the OGL.

-   -   a. Transcript level expression of Maize genes was measured by         analyzing transcriptome profiling data generated from Zea mays         c.v. B73 root and shoot tissues using RNAseq technology. For         each OGL, annotated genes within the Zea mays c.v. B73 genome         that were present in a 40 Kb neighborhood around the OGL were         identified. Expression levels for each of the genes in the         window were extracted from the transcriptome profiles and an         average gene expression level was calculated.

8. Level of Nucleosome occupancy around the OGL

-   -   a. Discerning the level of nucleosome occupancy for a particular         nucleotide sequence provides information about chromosomal         functions and the genomic context of the sequence. The NuPoP™         statistical package provides a user-friendly software tool for         predicting the nucleosome occupancy and the most probable         nucleosome positioning map for genomic sequences of any size         (Xi, L., Fondufe-Mittendor, Y., Xia, L., Flatow, J., Widom, J.         and Wang, J.-P., Predicting nucleosome positioning using a         duration Hidden Markov Model, BMC Bioinformatics, 2010,         doi:10.1186/1471-2105-11-346). For each OGL, the nucleotide         sequence was submitted to the NuPoP™ software and a nucleosome         occupancy score was calculated.

9. Relative location within the chromosome (proximity to centromere)

-   -   a. Information on position of the centromere in each of the         Maize chromosomes and the lengths of the chromosome arms was         extracted from Maize genome DB (www.maizegdb.org). For each OGL,         the genomic distance from the OGLsequence to the centromere of         the chromosome that it is located on, is measured (in bp). The         relative location of a OGL within the chromosome is represented         as the ratio of its genomic distance to the centromere relative         to the length of the specific chromosomal arm that it lies on.

10. Number of OGLs in a 1 Mb region around the OGL

-   -   a. For each OGL, a 1 Mb genomic window around the OGL location         is defined and the number of OGLs, in the Maize 1 Kb OGL         dataset, whose genomic locations overlap with this window is         tallied.

The results or values for the score of the features and attributes of each optimal nongenic maize genomic loci are further described in Table 3 of Example 2. The resulting dataset was used in the PCA statistical method to cluster the 5,286 identified optimal nongenic maize genomic loci into clusters. During the clustering process, after estimating the “p” principle components of the optimal genomic loci, the assignment of the optimal genomic loci to one of the 32 clusters proceeded in the “p” dimensional Euclidean space. Each of the “p” axes was divided into “k” intervals. Optimal genomic loci assigned to the same interval were grouped together to form clusters. Using this analysis, each PCA axis was divided into two intervals, which was chosen based on a priori information regarding the number of clusters required for experimental validation. All analysis and the visualization of the resulting clusters were carried out with the Molecular Operating Environment™ (MOE) software from Chemical Computing Group Inc. (Montreal, Quebec, Canada). The PCA approach was used to cluster the set of 5,286 optimal maize genomic loci into 32 distinct clusters based on their feature values, described above.

During the PCA process, five principal components (PC) were generated, with the top three PCs containing about 90% of the total variation in the dataset (Table 4). These three PCs were used to graphically represent the 32 clusters in a three dimensional plot (see FIG. 3). After the clustering process, was completed, one representative optimal genomic loci was chosen from each cluster. This was performed by choosing a select optimal genomic locus, within each cluster, that was closest to the centroid of that cluster by computational methods (Table 4). The chromosomal locations of the 32 representative optimal genomic loci are uniformly distributed among the maize chromosomes as shown in FIG. 4.

In accordance with one embodiment a purified optimal nongenic sequence is provided wherein the purified sequence is at least 1 Kb in length and has at least 90, 95%, or 99% sequence identity with a nongenic sequence selected from any sequence described in Table 15 of Example 8. In one embodiment the optimal nongenic maize genomic loci to be modified is a genomic sequence selected from loci_137693_G1 (SEQ ID NO:387), loci_265551_G1 (SEQ ID NO:463), loci_128078_G1 (SEQ ID NO:560), loci_168286_G1 (SEQ ID NO:573), loci_3733_G1 (SEQ ID NO:1268), loci_203075_G1 (SEQ ID NO:2030), loci_232484_G1 (SEQ ID NO:2053), loci_136086_G1 (SEQ ID NO:4425), loci_203704_G1 (SEQ ID NO:2033), loci_127268_G1 (SEQ ID NO:2709), loci_204637_G1 (SEQ ID NO:2731), loci_291068_G1 (SEQ ID NO:3230), loci_232222_G1 (SEQ ID NO:3357), loci_43577_G1 (SEQ ID NO:3428), loci_204726_G1 (SEQ ID NO:424), and loci_232228_G1 (SEQ ID NO: 4529). In one embodiment the purified sequence is at least 1 Kb in length and has at least 90%, 95%, or 99% sequence identity with a sequence present in a nongenic sequence selected from the group consisting of loci_137693_G1 (SEQ ID NO:387), loci_265551_G1 (SEQ ID NO:463), loci_128078_G1 (SEQ ID NO:560), loci_168286_G1 (SEQ ID NO:573), loci_3733_G1 (SEQ ID NO:1268), loci_203075_G1 (SEQ ID NO:2030), loci_232484_G1 (SEQ ID NO:2053), loci_136086_G1 (SEQ ID NO:4425), loci_203704_G1 (SEQ ID NO:2033), loci_127268_G1 (SEQ ID NO:2709), loci_204637_G1 (SEQ ID NO:2731), loci_291068_G1 (SEQ ID NO:3230), loci_232222_G1 (SEQ ID NO:3357), loci_43577_G1 (SEQ ID NO:3428), loci_204726_G1 (SEQ ID NO:424), and loci_232228_G1 (SEQ ID NO: 4529). In one embodiment a purified sequence is provided that is at least 1 Kb in length and has at least 90%, 95%, or 99% sequence identity with a sequence present in a nongenic sequence selected from the group consisting of optimal_loci_ 204637 (SEQ ID NO:2731), optimal_loci_136086 (SEQ ID NO:4425), optimal_loci_232484 (SEQ ID NO:2053), optimal_loci_203075 (SEQ ID NO:2030), optimal_loci_3733 (SEQ ID NO:1268), optimal_loci_168286 (SEQ ID NO:573), optimal_loci_128078 (SEQ ID NO:560), optimal_loci_265551 (SEQ ID NO:463), optimal_loci_127268 (SEQ ID NO:2709), optimal_loci_204726 (SEQ ID NO:424), and optimal_loci_232222 (SEQ ID NO:3357). In one embodiment a purified sequence is provided that is at least 1 Kb in length and has at least 90%, 95%, or 99% sequence identity with a sequence present in a nongenic sequence selected from the group consisting of optimal_loci_ 204637 (SEQ ID NO:2731), optimal_loci_136086 (SEQ ID NO:4425), optimal_loci_232484 (SEQ ID NO:2053), optimal_loci_203075 (SEQ ID NO:2030), optimal_loci_3733 (SEQ ID NO:1268), optimal_loci_168286 (SEQ ID NO:573), optimal_loci_128078 (SEQ ID NO:560) and optimal_loci_265551 (SEQ ID NO:463). In one embodiment a purified sequence is provided that is at least 1 Kb in length and has at least 90%, 95%, or 99% sequence identity with a sequence present in a nongenic sequence selected from the group consisting of optimal_loci_ 204637 (SEQ ID NO:2731), optimal_loci_203075 (SEQ ID NO:2030) and optimal_loci_128078 (SEQ ID NO:560).

In one embodiment a purified sequence is provided comprising a 1 Kb sequence identical to a sequence present in a nongenic sequence selected from the group consisting of optimal_loci_ 204637 (SEQ ID NO:2731), optimal_loci_136086 (SEQ ID NO:4425), optimal_loci_232484 (SEQ ID NO:2053), optimal_loci_203075 (SEQ ID NO:2030), optimal_loci_3733 (SEQ ID NO:1268), optimal_loci_168286 (SEQ ID NO:573), optimal_loci_128078 (SEQ ID NO:560) and optimal_loci_265551 (SEQ ID NO:463). In one embodiment a purified sequence is provided comprising a 1 Kb sequence identical to a sequence present in a nongenic sequence selected from the group consisting of optimal_loci_204637 (SEQ ID NO:2731), optimal_loci_203075 (SEQ ID NO:2030) and optimal_loci_128078 (SEQ ID NO:560).

In an embodiment, the subject disclosure relates to a recombinant sequence, comprising: a nucleic acid sequence of at least 1 Kb and having at least 90%, 95%, or 99% sequence identity with a nongenic sequence selected from the group consisting of loci_137693_G1 (SEQ ID NO:387), loci_265551_G1 (SEQ ID NO:463), loci_128078_G1 (SEQ ID NO:560), loci_168286_G1 (SEQ ID NO:573), loci_3733_G1 (SEQ ID NO:1268), loci_203075_G1 (SEQ ID NO:2030), loci_232484_G1 (SEQ ID NO:2053), and loci_204637_G1 (SEQ ID NO:2731), with a DNA of interest inserted into the nongenic sequence.

In accordance with one embodiment a modified optimal nongenic maize genomic loci is provided wherein the optimal nongenic maize genomic loci has been modified to comprise one or more nucleotide substitutions, deletions or insertions. In one embodiment the optimal nongenic maize genomic loci is modified by the insertion of a DNA of interest optionally accompanied with further nucleotide duplications, deletions or inversions of genomic loci sequence.

In an embodiment the optimal nongenic maize genomic loci to be modified is a genomic sequence selected from any sequence described in Table 15 of Example 8. In one embodiment the optimal nongenic maize genomic loci to be modified is a genomic sequence selected from loci_137693_G1 (SEQ ID NO:387), loci_265551_G1 (SEQ ID NO:463), loci_128078_G1 (SEQ ID NO:560), loci_168286_G1 (SEQ ID NO:573), loci_3733_G1 (SEQ ID NO:1268), loci_203075_G1 (SEQ ID NO:2030), loci_232484_G1 (SEQ ID NO:2053), loci_136086_G1 (SEQ ID NO:4425), loci_203704_G1 (SEQ ID NO:2033), loci_127268_G1 (SEQ ID NO:2709), loci_204637_G1 (SEQ ID NO:2731), loci_291068_G1 (SEQ ID NO:3230), loci_232222_G1 (SEQ ID NO:3357), loci_43577_G1 (SEQ ID NO:3428), loci_204726_G1 (SEQ ID NO:424), and loci_232228_G1 (SEQ ID NO: 4529). In one embodiment the optimal nongenic maize genomic loci to be modified is a genomic sequence from loci_137693_G1 (SEQ ID NO:387). In one embodiment the optimal nongenic maize genomic loci to be modified is a genomic sequence from loci_265551_G1 (SEQ ID NO:463). In one embodiment the optimal nongenic maize genomic loci to be modified is a genomic sequence from loci_128078_G1 (SEQ ID NO:560). In one embodiment the optimal nongenic maize genomic loci to be modified is a genomic sequence from loci_168286_G1 (SEQ ID NO:573). In one embodiment the optimal nongenic maize genomic loci to be modified is a genomic sequence from loci_3733_G1 (SEQ ID NO:1268). In one embodiment the optimal nongenic maize genomic loci to be modified is a genomic sequence from loci_203075_G1 (SEQ ID NO:2030). In one embodiment the optimal nongenic maize genomic loci to be modified is a genomic sequence from loci_232484_G1 (SEQ ID NO:2053). In one embodiment the optimal nongenic maize genomic loci to be modified is a genomic sequence from loci_136086_G1 (SEQ ID NO:4425). In one embodiment the optimal nongenic maize genomic loci to be modified is a genomic sequence from loci_203704_G1 (SEQ ID NO:2033). In one embodiment the optimal nongenic maize genomic loci to be modified is a genomic sequence from loci_127268_G1 (SEQ ID NO:2709). In one embodiment the optimal nongenic maize genomic loci to be modified is a genomic sequence s from loci_204637_G1 (SEQ ID NO:2731). In one embodiment the optimal nongenic maize genomic loci to be modified is a genomic sequence from loci_291068_G1 (SEQ ID NO:3230). In one embodiment the optimal nongenic maize genomic loci to be modified is a genomic sequence from loci_232222_G1 (SEQ ID NO:3357). In one embodiment the optimal nongenic maize genomic loci to be modified is a genomic sequence from loci_43577_G1 (SEQ ID NO:3428). In one embodiment the optimal nongenic maize genomic loci to be modified is a genomic sequence from loci_204726_G1 (SEQ ID NO:424). In one embodiment the optimal nongenic maize genomic loci to be modified is a genomic sequence from loci_232228_G1 (SEQ ID NO: 4529).

In a further embodiment the optimal nongenic maize genomic loci to be modified is a genomic sequence selected from loci_137693_G1 (SEQ ID NO:387), loci_265551_G1 (SEQ ID NO:463), loci_128078_G1 (SEQ ID NO:560), loci_168286_G1 (SEQ ID NO:573), loci_3733_G1 (SEQ ID NO:1268), loci_203075_G1 (SEQ ID NO:2030), loci_232484_G1 (SEQ ID NO:2053), loci_136086_G1 (SEQ ID NO:4425), and loci_203704_G1 (SEQ ID NO:2033). In a further embodiment the optimal nongenic maize genomic loci to be modified is a genomic sequence selected from loci_137693_G1 (SEQ ID NO:387), loci_265551_G1 (SEQ ID NO:463), loci_128078_G1 (SEQ ID NO:560), loci_168286_G1 (SEQ ID NO:573), loci_3733_G1 (SEQ ID NO:1268), loci_203075_G1 (SEQ ID NO:2030), loci_232484_G1 (SEQ ID NO:2053), and loci_136086_G1 (SEQ ID NO:4425). In a further embodiment the optimal nongenic maize genomic loci to be modified is a genomic sequence selected from loci_137693_G1 (SEQ ID NO:387), loci_265551_G1 (SEQ ID NO:463), loci_128078_G1 (SEQ ID NO:560), loci_168286_G1 (SEQ ID NO:573), loci_3733_G1 (SEQ ID NO:1268), loci_203075_G1 (SEQ ID NO:2030), and loci_232484_G1 (SEQ ID NO:2053). In a further embodiment the optimal nongenic maize genomic loci to be modified is a genomic sequence selected from loci_137693_G1 (SEQ ID NO:387), loci_265551_G1 (SEQ ID NO:463), loci_128078_G1 (SEQ ID NO:560), loci_168286_G1 (SEQ ID NO:573), loci_3733_G1 (SEQ ID NO:1268), and loci_203075_G1 (SEQ ID NO:2030). In a further embodiment the optimal nongenic maize genomic loci to be modified is a genomic sequence selected from loci_137693_G1 (SEQ ID NO:387), loci_265551_G1 (SEQ ID NO:463), loci_128078_G1 (SEQ ID NO:560), loci_168286_G1 (SEQ ID NO:573), and loci_3733_G1 (SEQ ID NO:1268). In a further embodiment the optimal nongenic maize genomic loci to be modified is a genomic sequence selected from loci_137693_G1 (SEQ ID NO:387), loci_265551_G1 (SEQ ID NO:463), loci_128078_G1 (SEQ ID NO:560), and loci_168286_G1 (SEQ ID NO:573). In a further embodiment the optimal nongenic maize genomic loci to be modified is a genomic sequence selected from loci_137693_G1 (SEQ ID NO:387), loci_265551_G1 (SEQ ID NO:463), and loci_128078_G1 (SEQ ID NO:560). In a further embodiment the optimal nongenic maize genomic loci to be modified is a genomic sequence selected from loci_137693_G1 (SEQ ID NO:387), and loci_265551_G1 (SEQ ID NO:463).

In a further embodiment the optimal nongenic maize genomic loci to be modified is a genomic sequence selected from loci_127268_G1 (SEQ ID NO:2709), loci_204637_G1 (SEQ ID NO:2731), loci_291068_G1 (SEQ ID NO:3230), loci_232222_G1 (SEQ ID NO:3357), loci_43577_G1 (SEQ ID NO:3428), loci_204726_G1 (SEQ ID NO:424), and loci_232228_G1 (SEQ ID NO: 4529). In a further embodiment the optimal nongenic maize genomic loci to be modified is a genomic sequence selected from loci_127268_G1 (SEQ ID NO:2709), loci_204637_G1 (SEQ ID NO:2731), loci_291068_G1 (SEQ ID NO:3230), loci_232222_G1 (SEQ ID NO:3357), loci_43577_G1 (SEQ ID NO:3428), and loci_204726_G1 (SEQ ID NO:424). In a further embodiment the optimal nongenic maize genomic loci to be modified is a genomic sequence selected from loci_127268_G1 (SEQ ID NO:2709), loci_204637_G1 (SEQ ID NO:2731), loci_291068_G1 (SEQ ID NO:3230), loci_232222_G1 (SEQ ID NO:3357), and loci_43577_G1 (SEQ ID NO:3428). In a further embodiment the optimal nongenic maize genomic loci to be modified is a genomic sequence selected from loci_127268_G1 (SEQ ID NO:2709), loci_204637_G1 (SEQ ID NO:2731), loci_291068_G1 (SEQ ID NO:3230), and loci_232222_G1 (SEQ ID NO:3357). In a further embodiment the optimal nongenic maize genomic loci to be modified is a genomic sequence selected from loci_127268_G1 (SEQ ID NO:2709), loci_204637_G1 (SEQ ID NO:2731), and loci_291068_G1 (SEQ ID NO:3230). In a further embodiment the optimal nongenic maize genomic loci to be modified is a genomic sequence selected from loci_127268_G1 (SEQ ID NO:2709), and loci_204637_G1 (SEQ ID NO:2731).

In one embodiment the optimal nongenic maize genomic loci is selected from the genomic sequences of loci_59517_G1 (SEQ ID NO: 1), loci_159525_G1 (SEQ ID NO: 199), loci_9811_G1 (SEQ ID NO: 365), loci_7507_G1 (SEQ ID NO: 543), loci_178978_G1 (SEQ ID NO: 687), loci_285621_G1 (SEQ ID NO: 875), loci_221721_G1 (SEQ ID NO: 1089), loci_83937_G1 (SEQ ID NO: 1233), loci_37146_G1 (SEQ ID NO: 1369), loci_156393_G1 (SEQ ID NO: 1571), loci_343678_G1 (SEQ ID NO: 1795), loci_60209_G1 (SEQ ID NO: 1980), loci_282323_G1 (SEQ ID NO: 2171), loci_64542_G1 (SEQ ID NO: 2349), loci_162531_G1 (SEQ ID NO: 2557), loci_337001_G1 (SEQ ID NO: 2693), loci_66202_G1 (SEQ ID NO: 2855), loci_185454_G1 (SEQ ID NO: 3004), loci_239863_G1 (SEQ ID NO: 3151), loci_257541_G1 (SEQ ID NO: 3289), loci_217939_G1 (SEQ ID NO: 3455), loci_326869_G1 (SEQ ID NO: 3586), loci_31710_G1 (SEQ ID NO: 3731), loci_81941_G1 (SEQ ID NO: 3849), loci_198387_G1 (SEQ ID NO: 3981), loci_197372_G1 (SEQ ID NO: 4192), loci_106202_G1 (SEQ ID NO: 4401), loci_232228_G1 (SEQ ID NO: 4529), loci_244324_G1 (SEQ ID NO: 4646), loci_157315_G1 (SEQ ID NO: 4836), loci_137489_G1 (SEQ ID NO: 5046), and loci_31764_G1 (SEQ ID NO: 5162).

In one embodiment the optimal nongenic maize genomic loci is selected from the genomic sequences of loci_59517_G1 (SEQ ID NO: 1), loci_25001_G1 (SEQ ID NO: 100), loci_112632_G1 (SEQ ID NO: 203), loci_28905_G1 (SEQ ID NO: 295), loci_129164_G1 (SEQ ID NO: 384), loci_204726_G1 (SEQ ID NO: 424), loci_2425_G1 (SEQ ID NO: 451), loci_122036_G1 (SEQ ID NO: 547), loci_5735_G1 (SEQ ID NO: 671), loci_178978_G1 (SEQ ID NO: 687), loci_288388_G1 (SEQ ID NO: 781), loci_60310_G1 (SEQ ID NO: 843), loci_285621_G1 (SEQ ID NO: 875), loci_243330_G1 (SEQ ID NO: 967), loci_127038_G1 (SEQ ID NO: 1107), loci_262784_G1 (SEQ ID NO: 1147), loci_344662_G1 (SEQ ID NO: 1190), loci_153894_G1 (SEQ ID NO: 1252), loci_28771_G1 (SEQ ID NO: 1300), loci_1098_G1 (SEQ ID NO: 1371), loci_97772_G1 (SEQ ID NO: 1569), loci_156393_G1 (SEQ ID NO: 1571), loci_236662_G1 (SEQ ID NO: 1663), loci_139485_G1 (SEQ ID NO: 1822), loci_301175_G1 (SEQ ID NO: 1906), loci_152337_G1 (SEQ ID NO: 2003), loci_202616_G1 (SEQ ID NO: 2027), loci_203704_G1 (SEQ ID NO: 2033), loci_282323_G1 (SEQ ID NO: 2171), loci_262782_G1 (SEQ ID NO: 2256), loci_64542_G1 (SEQ ID NO: 2349), loci_236455_G1 (SEQ ID NO: 2428), loci_162531_G1 (SEQ ID NO: 2557), loci_301774_G1 (SEQ ID NO: 2632), loci_344663_G1 (SEQ ID NO: 2649), loci_337001_G1 (SEQ ID NO: 2693), loci_204637_G1 (SEQ ID NO: 2731), loci_238100_G1 (SEQ ID NO: 2753), loci_66202_G1 (SEQ ID NO: 2855), loci_264359_G1 (SEQ ID NO: 2934), loci_282653_G1 (SEQ ID NO: 3086), loci_80282_G1 (SEQ ID NO: 3139), loci_291068_G1 (SEQ ID NO: 3230), loci_56395_G1 (SEQ ID NO: 3270), loci_200497_G1 (SEQ ID NO: 3334), loci_232222_G1 (SEQ ID NO: 3357), loci_43577_G1 (SEQ ID NO: 3428), loci_5607_G1 (SEQ ID NO: 3435), loci_114664_G1 (SEQ ID NO: 3457), loci_228254_G1 (SEQ ID NO: 3497), loci_120993_G1 (SEQ ID NO: 3593), loci_53137_G1 (SEQ ID NO: 3702), loci_31710_G1 (SEQ ID NO: 3731), loci_344664_G1 (SEQ ID NO: 3815), loci_81941_G1 (SEQ ID NO: 3849), loci_321514_G1 (SEQ ID NO: 3939), loci_198387_G1 (SEQ ID NO: 3981), loci_301180_G1 (SEQ ID NO: 4113), loci_197372_G1 (SEQ ID NO: 4192), loci_348776_G1 (SEQ ID NO: 4350), loci_244439_G1 (SEQ ID NO: 4458), loci_348258_G1 (SEQ ID NO: 4487), loci_232228_G1 (SEQ ID NO: 4529), loci_322501_G1 (SEQ ID NO: 4610), loci_244324_G1 (SEQ ID NO: 4646), loci_97232_G1 (SEQ ID NO: 4832), loci_157315_G1 (SEQ ID NO: 4836), loci_282499_G1 (SEQ ID NO: 4953), loci_155031_G1 (SEQ ID NO: 5060), loci_301773_G1 (SEQ ID NO: 5110), loci_283161_G1 (SEQ ID NO:5213), loci_55524_G1 (SEQ ID NO: 5264), loci_127268_G1 (SEQ ID NO:2709), loci_136086_G1 (SEQ ID NO: 4425), loci_232484_G1 (SEQ ID NO: 2053), loci_3733_G1 (SEQ ID NO: 1923), loci_168286_G1 (SEQ ID NO:3473571573), loci_128078_G1 (SEQ ID NO:3047560), loci_265551_G1 (SEQ ID NO:4163), and loci_137693_G1 (SEQ ID NO:387).

In one embodiment the optimal nongenic maize genomic loci is targeted with a DNA of interest, wherein the DNA of interest integrates within or proximal to the zinc finger nuclease target sites. In accordance with an embodiment, exemplary zinc finger target sites of optimal maize select genomic loci are provided in Table 8. In accordance with an embodiment, integration of a DNA of interest occurs within or proximal to the exemplary target sites of: 111879ZFN5 and 111879ZFN7; 111885ZFN1 and 111885ZFN2; SIG115737_31 v1 and SIG115737_32 v1; SIG120523_11 v1 and SIG120523_12 v1; SIG115246_5 and SIG115246_6; SIG115636_1 v1 and SIG115636_2 v1; SIG120417_11 v1 and SIG120417_12 v1; SIG120621_15 v1 and SIG120621_16 v1; SIG12078_11 v1 and SIG12078_12 v1; and, SIG157315_1 v1 and SIG157315_2 v1, ZFN_binding_1 and ZFN_binding_2, ZFN_binding_3 and ZFN_binding_4, ZFN_binding_5 and ZFN_binding_6, ZFN_binding_7 and ZFN_binding_8, ZFN_binding_9 and ZFN_binding_10, ZFN_binding_11 and ZFN_binding_12, ZFN_binding_13 and ZFN_binding_14, ZFN_binding_15 and ZFN_binding_16, ZFN_binding_17 and ZFN_binding_18, ZFN_binding_19 and ZFN_binding_20, ZFN_binding_21 and ZFN_binding_22, ZFN_binding_23 and ZFN_binding_24, ZFN_binding_25 and ZFN_binding_26, ZFN_binding_27 and ZFN_binding_28, ZFN_binding_29 and ZFN_binding_30, ZFN_binding_31 and ZFN_binding_32, ZFN_binding_33 and ZFN_binding_34, ZFN_binding_35 and ZFN_binding_36, ZFN_binding_37 and ZFN_binding_38, ZFN_binding_39 and ZFN_binding_40, ZFN_binding_41 and ZFN_binding_42, ZFN_binding_43 and ZFN_binding_44, ZFN_binding_45 and ZFN_binding_46, ZFN_binding_47 and ZFN_binding_48, ZFN_binding_49 and ZFN_binding_50, ZFN_binding_51 and ZFN_binding_52, ZFN_binding_53 and ZFN_binding_54, ZFN_binding_55 and ZFN_binding_56, ZFN_binding_57 and ZFN_binding_58, ZFN_binding_59 and ZFN_binding_60, ZFN_binding_61 and ZFN_binding_62, ZFN_binding_63 and ZFN_binding_64, ZFN_binding_65 and ZFN_binding_66, ZFN_binding_67 and ZFN_binding_68, ZFN_binding_69 and ZFN_binding_70, ZFN_binding_71 and ZFN_binding_72, ZFN_binding_73 and ZFN_binding_74, ZFN_binding_75 and ZFN_binding_76, ZFN_binding_77 and ZFN_binding_78, ZFN_binding_79 and ZFN_binding_80, ZFN_binding_81 and ZFN_binding_82, ZFN_binding_83 and ZFN_binding_84, ZFN_binding_85 and ZFN_binding_86, ZFN_binding_87 and ZFN_binding_88, ZFN_binding_89 and ZFN_binding_90, ZFN_binding_91 and ZFN_binding_92, ZFN_binding_93 and ZFN_binding_94, ZFN_binding_95 and ZFN_binding_96, ZFN_binding_97 and ZFN_binding_98, ZFN_binding_99 and ZFN_binding_100, ZFN_binding_101 and ZFN_binding_102, ZFN_binding_103 and ZFN_binding_104, ZFN_binding_105 and ZFN_binding_106, ZFN_binding_107 and ZFN_binding_108, ZFN_binding_109 and ZFN_binding_110, ZFN_binding_111 and ZFN_binding_112, ZFN_binding_113 and ZFN_binding_114, ZFN_binding_115 and ZFN_binding_116, ZFN_binding_117 and ZFN_binding_118, ZFN_binding_119 and ZFN_binding_120, ZFN_binding_121 and ZFN_binding_122, ZFN_binding_123 and ZFN_binding_124, ZFN_binding_125 and ZFN_binding_126, ZFN_binding_127 and ZFN_binding_128, ZFN_binding_129 and ZFN_binding_130, ZFN_binding_131 and ZFN_binding_132.

In accordance with an embodiment, the zinc finger nuclease binds to the zinc finger target site and cleaves the unique maize genomic polynucleotide target sites, whereupon the DNA of interest integrates within or proximal to the maize genomic polynucleotide target sites. In an embodiment, integration of the DNA of interest occurs within the zinc finger target site may result with rearrangements. In accordance with one embodiment, the rearrangements may comprise deletions, insertions, inversions, and repeats. In an embodiment, integration of the DNA of interest occurs proximal to the zinc finger target site. According to an aspect of the embodiment, the integration of the DNA is proximal to the zinc finger target site, and may integrate within 1.5 Kb, 1.25 Kb, 1.0 Kb, 0.75 Kb, 0.5 Kb, or 0.25 Kb to the zinc finger target site. Insertion within a genomic region proximal to the zinc finger target site is known in the art, see US Patent Pub No. 2010/0257638 A1 (herein incorporated by reference in its entirety).

In accordance with one embodiment the selected nongenic sequence comprises the following characteristics:

a) the nongenic sequence does not contain greater than 1% DNA methylation within the sequence;

b) the nongenic sequence has a relative location value from 0.0984 to 0.973 ratio of genomic distance from a maize chromosomal centromere;

c) the nongenic sequence has a guanine/cytosine percent content range of 34.38 to 61.2%; and,

d) the nongenic sequence is from about 1 Kb to about 4.9 Kb in length.

II. Recombinant Derivatives of Identified Optimal Nongenic Maize Genomic Loci

In accordance with one embodiment, after having identified a genomic loci of Zea mays as a highly desirable location for inserting polynucleotide donor sequences, one or more nucleic acids of interest can be inserted into the identified genomic locus. In one embodiment the nucleic acid of interest comprises exogenous gene sequences or other desirable polynucleotide donor sequences. In another embodiment, after having identified a genomic loci of Zea mays as a highly desirable location for inserting polynucleotide donor sequences, one or more nucleic acids of interest of the optimal nongenic maize genomic loci can optionally be deleted, excised or removed with the subsequent integration of the DNA of interest into the identified genomic locus. In one embodiment the insertion of a nucleic acid of interest into the optimal nongenic maize genomic loci comprises removal, deletion, or excision of the exogenous gene sequences or other desirable polynucleotide donor sequences.

The present disclosure further relates to methods and compositions for targeted integration into the select Zea mays genomic locus using ZFNs and a polynucleotide donor construct. The methods for inserting a nucleic acid sequence of interest into the optimal nongenic maize genomic loci, unless otherwise indicated, use conventional techniques in molecular biology, biochemistry, chromatin structure and analysis, cell culture, recombinant DNA and related fields as are within the skill of the art. These techniques are fully explained in the literature. See, for example, Sambrook et al. MOLECULAR CLONING: A LABORATORY MANUAL, Second edition, Cold Spring Harbor Laboratory Press, 1989 and Third edition, 2001; Ausubel et al., CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, John Wiley & Sons, New York, 1987 and periodic updates; the series METHODS IN ENZYMOLOGY, Academic Press, San Diego; Wolfe, CHROMATIN STRUCTURE AND FUNCTION, Third edition, Academic Press, San Diego, 1998; METHODS IN ENZYMOLOGY, Vol. 304, “Chromatin” (P. M. Wassarman and A. P. Wolffe, eds.), Academic Press, San Diego, 1999; and METHODS IN MOLECULAR BIOLOGY, Vol. 119, “Chromatin Protocols” (P. B. Becker, ed.) Humana Press, Totowa, 1999.

Methods for Nucleic Acid Insertion into the Maize Genome

Any of the well known procedures for introducing polynucleotide donor sequences and nuclease sequences as a DNA construct into host cells may be used in accordance with the present disclosure. These include the use of calcium phosphate transfection, polybrene, protoplast fusion, PEG, electroporation, ultrasonic methods (e.g., sonoporation), liposomes, microinjection, naked DNA, plasmid vectors, viral vectors, both episomal and integrative, and any of the other well known methods for introducing cloned genomic DNA, cDNA, synthetic DNA or other foreign genetic material into a host cell (see, e.g., Sambrook et al., supra). It is only necessary that the particular nucleic acid insertion procedure used be capable, of successfully introducing at least one gene into the host cell capable of expressing the protein of choice.

As noted above, DNA constructs may be introduced into the genome of a desired plant species by a variety of conventional techniques. For reviews of such techniques see, for example, Weissbach & Weissbach Methods for Plant Molecular Biology (1988, Academic Press, N.Y.) Section VIII, pp. 421-463; and Grierson & Corey, Plant Molecular Biology (1988, 2d Ed.), Blackie, London, Ch. 7-9. A DNA construct may be introduced directly into the genomic DNA of the plant cell using techniques such as electroporation and microinjection of plant cell protoplasts, by agitation with silicon carbide fibers (See, e.g., U.S. Pat. Nos. 5,302,523 and 5,464,765), or the DNA constructs can be introduced directly to plant tissue using biolistic methods, such as DNA particle bombardment (see, e.g., Klein et al. (1987) Nature 327:70-73). Alternatively, the DNA construct can be introduced into the plant cell via nanoparticle transformation (see, e.g., US Patent Publication No. 20090104700, which is incorporated herein by reference in its entirety). Alternatively, the DNA constructs may be combined with suitable T-DNA border/flanking regions and introduced into a conventional Agrobacterium tumefaciens host vector. Agrobacterium tumefaciens-mediated transformation techniques, including disarming and use of binary vectors, are well described in the scientific literature. See, for example Horsch et al. (1984) Science 233:496-498, and Fraley et al. (1983) Proc. Nat'l. Acad. Sci. USA 80:4803.

In addition, gene transfer may be achieved using non-Agrobacterium bacteria or viruses such as Rhizobium sp. NGR234, Sinorhizoboium meliloti, Mesorhizobium loti, potato virus X, cauliflower mosaic virus and cassava vein mosaic virus and/or tobacco mosaic virus, See, e.g., Chung et al. (2006) Trends Plant Sci. 11(1):1-4. The virulence functions of the Agrobacterium tumefaciens host will direct the insertion of a T-strand containing the construct and adjacent marker into the plant cell DNA when the cell is infected by the bacteria using binary T DNA vector (Bevan (1984) Nuc. Acid Res. 12:8711-8721) or the co-cultivation procedure (Horsch et al. (1985) Science 227:1229-1231). Generally, the Agrobacterium transformation system is used to engineer dicotyledonous plants (Bevan et al. (1982) Ann. Rev. Genet. 16:357-384; Rogers et al. (1986) Methods Enzymol. 118:627-641). The Agrobacterium transformation system may also be used to transform, as well as transfer, DNA to monocotyledonous plants and plant cells. See U.S. Pat. No. 5,591,616; Hernalsteen et al. (1984) EMBO J. 3:3039-3041; Hooykass-Van Slogteren et al. (1984) Nature 311:763-764; Grimsley et al. (1987) Nature 325:1677-179; Boulton et al. (1989) Plant Mol. Biol. 12:31-40; and Gould et al. (1991) Plant Physiol. 95:426-434.

Alternative gene transfer and transformation methods include, but are not limited to, protoplast transformation through calcium-, polyethylene glycol (PEG)- or electroporation-mediated uptake of naked DNA (see Paszkowski et al. (1984) EMBO J. 3:2717-2722, Potrykus et al. (1985) Molec. Gen. Genet. 199:169-177; Fromm et al. (1985) Proc. Nat. Acad. Sci. USA 82:5824-5828; and Shimamoto (1989) Nature 338:274-276) and electroporation of plant tissues (D'Halluin et al. (1992) Plant Cell 4:1495-1505). Additional methods for plant cell transformation include microinjection, silicon carbide mediated DNA uptake (Kaeppler et al. (1990) Plant Cell Reporter 9:415-418), and microprojectile bombardment (see Klein et al. (1988) Proc. Nat. Acad. Sci. USA 85:4305-4309; and Gordon-Kamm et al. (1990) Plant Cell 2:603-618).

In one embodiment a nucleic acid of interest introduced into a host cell for targeted insertion into the genome comprises homologous flanking sequences on one or both ends of the targeted nucleic acid of interest. In such an embodiment, the homologous flanking sequences contain sufficient levels of sequence identity to a maize genomic sequence to support homologous recombination between it and the genomic sequence to which it bears homology. Approximately 25, 50, 100, 200, 500, 750, 1000, 1500, or 2000 nucleotides, or more of sequence identity, ranging from 70% to 100%, between a donor and a genomic sequence (or any integral value between 10 and 200 nucleotides, or more) will support homologous recombination therebetween.

In another embodiment the targeted nucleic acid of interest lacks homologous flanking sequences, and the targeted nucleic acid of interest shares low to very low levels of sequence identity with a genomic sequence.

In other embodiments of targeted recombination and/or replacement and/or alteration of a sequence in a region of interest in cellular chromatin, a chromosomal sequence is altered by homologous recombination with an exogenous “donor” nucleotide sequence. Such homologous recombination is stimulated by the presence of a double-stranded break in cellular chromatin, if sequences homologous to the region of the break are present. Double-strand breaks in cellular chromatin can also stimulate cellular mechanisms of non-homologous end joining. In any of the methods described herein, the first nucleotide sequence (the “donor sequence”) can contain sequences that are homologous, but not identical, to genomic sequences in the region of interest, thereby stimulating homologous recombination to insert a non-identical sequence in the region of interest. Thus, in certain embodiments, portions of the donor sequence that are homologous to sequences in the region of interest exhibit between about 80, 85, 90, 95, 97.5, to 99% (or any integer therebetween) sequence identity to the genomic sequence that is replaced. In other embodiments, the homology between the donor and genomic sequence is higher than 99%, for example if only 1 nucleotide differs as between donor and genomic sequences of over 100 contiguous base pairs.

In certain cases, a non-homologous portion of the donor sequence can contain sequences not present in the region of interest, such that new sequences are introduced into the region of interest. In these instances, the non-homologous sequence is generally flanked by sequences of 50 to 2,000 base pairs (or any integral value therebetween) or any number of base pairs greater than 2,000, that are homologous or identical to sequences in the region of interest. In other embodiments, the donor sequence is non-homologous to the region of interest, and is inserted into the genome by non-homologous recombination mechanisms.

In accordance with one embodiment a zinc finger nuclease (ZFN) is used to introduce a double strand break in a targeted genomic locus to facilitate the insertion of a nucleic acid of interest. Selection of a target site within the selected genomic locus for binding by a zinc finger domain can be accomplished, for example, according to the methods disclosed in U.S. Pat. No. 6,453,242, the disclosure of which is incorporated herein, that also discloses methods for designing zinc finger proteins (ZFPs) to bind to a selected sequence. It will be clear to those skilled in the art that simple visual inspection of a nucleotide sequence can also be used for selection of a target site. Accordingly, any means for target site selection can be used in the methods described herein.

For ZFP DNA-binding domains, target sites are generally composed of a plurality of adjacent target subsites. A target subsite refers to the sequence, usually either a nucleotide triplet or a nucleotide quadruplet which may overlap by one nucleotide with an adjacent quadruplet that is bound by an individual zinc finger. See, for example, WO 02/077227, the disclosure of which is incorporated herein. A target site generally has a length of at least 9 nucleotides and, accordingly, is bound by a zinc finger binding domain comprising at least three zinc fingers. However binding of, for example, a 4-finger binding domain to a 12-nucleotide target site, a 5-finger binding domain to a 15-nucleotide target site or a 6-finger binding domain to an 18-nucleotide target site, is also possible. As will be apparent, binding of larger binding domains (e.g., 7-, 8-, 9-finger and more) to longer target sites is also consistent with the subject disclosure.

In accordance with one embodiment, it is not necessary for a target site to be a multiple of three nucleotides. In cases in which cross-strand interactions occur (see, e.g., U.S. Pat. No. 6,453,242 and WO 02/077227), one or more of the individual zinc fingers of a multi-finger binding domain can bind to overlapping quadruplet subsites. As a result, a three-finger protein can bind a 10-nucleotide sequence, wherein the tenth nucleotide is part of a quadruplet bound by a terminal finger, a four-finger protein can bind a 13-nucleotide sequence, wherein the thirteenth nucleotide is part of a quadruplet bound by a terminal finger, etc.

The length and nature of amino acid linker sequences between individual zinc fingers in a multi-finger binding domain also affects binding to a target sequence. For example, the presence of a so-called “non-canonical linker,” “long linker” or “structured linker” between adjacent zinc fingers in a multi-finger binding domain can allow those fingers to bind subsites which are not immediately adjacent. Non-limiting examples of such linkers are described, for example, in U.S. Pat. No. 6,479,626 and WO 01/53480. Accordingly, one or more subsites, in a target site for a zinc finger binding domain, can be separated from each other by 1, 2, 3, 4, 5 or more nucleotides. One nonlimiting example would be a four-finger binding domain that binds to a 13-nucleotide target site comprising, in sequence, two contiguous 3-nucleotide subsites, an intervening nucleotide, and two contiguous triplet subsites.

While DNA-binding polypeptides identified from proteins that exist in nature typically bind to a discrete nucleotide sequence or motif (e.g., a consensus recognition sequence), methods exist and are known in the art for modifying many such DNA-binding polypeptides to recognize a different nucleotide sequence or motif. DNA-binding polypeptides include, for example and without limitation: zinc finger DNA-binding domains; leucine zippers; UPA DNA-binding domains; GAL4; TAL; LexA; a Tet repressor; LacR; and a steroid hormone receptor.

In some examples, a DNA-binding polypeptide is a zinc finger. Individual zinc finger motifs can be designed to target and bind specifically to any of a large range of DNA sites. Canonical Cys₂His₂ (as well as non-canonical Cys₃His) zinc finger polypeptides bind DNA by inserting an α-helix into the major groove of the target DNA double helix. Recognition of DNA by a zinc finger is modular; each finger contacts primarily three consecutive base pairs in the target, and a few key residues in the polypeptide mediate recognition. By including multiple zinc finger DNA-binding domains in a targeting endonuclease, the DNA-binding specificity of the targeting endonuclease may be further increased (and hence the specificity of any gene regulatory effects conferred thereby may also be increased). See, e.g., Urnov et al. (2005) Nature 435:646-51. Thus, one or more zinc finger DNA-binding polypeptides may be engineered and utilized such that a targeting endonuclease introduced into a host cell interacts with a DNA sequence that is unique within the genome of the host cell. Preferably, the zinc finger protein is non-naturally occurring in that it is engineered to bind to a target site of choice. See, for example, Beerli et al. (2002) Nature Biotechnol. 20:135-141; Pabo et al. (2001) Ann. Rev. Biochem. 70:313-340; Isalan et al. (2001) Nature Biotechnol. 19:656-660; Segal et al. (2001) Curr. Opin. Biotechnol. 12:632-637; Choo et al. (2000) Curr. Opin. Struct. Biol. 10:411-416; U.S. Pat. Nos. 6,453,242; 6,534,261; 6,599,692; 6,503,717; 6,689,558; 7,030,215; 6,794,136; 7,067,317; 7,262,054; 7,070,934; 7,361,635; 7,253,273; and U.S. Patent Publication Nos. 2005/0064474; 2007/0218528; 2005/0267061, all incorporated herein by reference in their entireties.

An engineered zinc finger binding domain can have a novel binding specificity, compared to a naturally-occurring zinc finger protein. Engineering methods include, but are not limited to, rational design and various types of selection. Rational design includes, for example, using databases comprising triplet (or quadruplet) nucleotide sequences and individual zinc finger amino acid sequences, in which each triplet or quadruplet nucleotide sequence is associated with one or more amino acid sequences of zinc fingers which bind the particular triplet or quadruplet sequence. See, for example, co-owned U.S. Pat. Nos. 6,453,242 and 6,534,261, incorporated by reference herein in their entireties.

Alternatively, the DNA-binding domain may be derived from a nuclease. For example, the recognition sequences of homing endonucleases and meganucleases such as I-SceI, I-CeuI, PI-PspI, PI-Sce, I-SceIV, I-CsmI, I-PanI, I-SceII, I-PpoI, I-SceIII, I-CreI, I-TevI, I-TevII and I-TevIII are known. See also U.S. Pat. Nos. 5,420,032; 6,833,252; Belfort et al. (1997) Nucleic Acids Res. 25:3379-3388; Dujon et al. (1989) Gene 82:115-118; Perler et al. (1994) Nucleic Acids Res. 22, 1125-1127; Jasin (1996) Trends Genet. 12:224-228; Gimble et al. (1996) J. Mol. Biol. 263:163-180; Argast et al. (1998) J. Mol. Biol. 280:345-353 and the New England Biolabs catalogue. In addition, the DNA-binding specificity of homing endonucleases and meganucleases can be engineered to bind non-natural target sites. See, for example, Chevalier et al. (2002) Molec. Cell 10:895-905; Epinat et al. (2003) Nucleic Acids Res. 31:2952-2962; Ashworth et al. (2006) Nature 441:656-659; Paques et al. (2007) Current Gene Therapy 7:49-66; U.S. Patent Publication No. 20070117128.

As another alternative, the DNA-binding domain may be derived from a leucine zipper protein. Leucine zippers are a class of proteins that are involved in protein-protein interactions in many eukaryotic regulatory proteins that are important transcription factors associated with gene expression. The leucine zipper refers to a common structural motif shared in these transcriptional factors across several kingdoms including animals, plants, yeasts, etc. The leucine zipper is formed by two polypeptides (homodimer or heterodimer) that bind to specific DNA sequences in a manner where the leucine residues are evenly spaced through an α-helix, such that the leucine residues of the two polypeptides end up on the same face of the helix. The DNA binding specificity of leucine zippers can be utilized in the DNA-binding domains disclosed herein.

In some embodiments, the DNA-binding domain is an engineered domain from a TAL effector derived from the plant pathogen Xanthomonas (see, Miller et al. (2011) Nature Biotechnology 29(2):143-8; Boch et al, (2009) Science 29 Oct. 2009 (10.1126/science.117881) and Moscou and Bogdanove, (2009) Science 29 Oct. 2009 (10.1126/science.1178817; and U.S. Patent Publication Nos. 20110239315, 20110145940 and 20110301073).

The CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas (CRISPR Associated) nuclease system is a recently engineered nuclease system based on a bacterial system that can be used for genome engineering. It is based on part of the adaptive immune response of many bacteria and Archea. When a virus or plasmid invades a bacterium, segments of the invader's DNA are converted into CRISPR RNAs (crRNA) by the ‘immune’ response. This crRNA then associates, through a region of partial complementarity, with another type of RNA called tracrRNA to guide the Cas9 nuclease to a region homologous to the crRNA in the target DNA called a “protospacer”. Cas9 cleaves the DNA to generate blunt ends at the DSB at sites specified by a 20-nucleotide guide sequence contained within the crRNA transcript. Cas9 requires both the crRNA and the tracrRNA for site specific DNA recognition and cleavage. This system has now been engineered such that the crRNA and tracrRNA can be combined into one molecule (the “single guide RNA”), and the crRNA equivalent portion of the single guide RNA can be engineered to guide the Cas9 nuclease to target any desired sequence (see Jinek et al (2012) Science 337, p. 816-821, Jinek et al, (2013), eLife 2:e00471, and David Segal, (2013) eLife 2:e00563). Thus, the CRISPR/Cas system can be engineered to create a double-stranded break (DSB) at a desired target in a genome, and repair of the DSB can be influenced by the use of repair inhibitors to cause an increase in error prone repair.

In certain embodiments, Cas protein may be a “functional derivative” of a naturally occurring Cas protein. A “functional derivative” of a native sequence polypeptide is a compound having a qualitative biological property in common with a native sequence polypeptide. “Functional derivatives” include, but are not limited to, fragments of a native sequence and derivatives of a native sequence polypeptide and its fragments, provided that they have a biological activity in common with a corresponding native sequence polypeptide. A biological activity contemplated herein is the ability of the functional derivative to hydrolyze a DNA substrate into fragments. The term “derivative” encompasses both amino acid sequence variants of polypeptide, covalent modifications, and fusions thereof. Suitable derivatives of a Cas polypeptide or a fragment thereof include but are not limited to mutants, fusions, covalent modifications of Cas protein or a fragment thereof. Cas protein, which includes Cas protein or a fragment thereof, as well as derivatives of Cas protein or a fragment thereof, may be obtainable from a cell or synthesized chemically or by a combination of these two procedures. The cell may be a cell that naturally produces Cas protein, or a cell that naturally produces Cas protein and is genetically engineered to produce the endogenous Cas protein at a higher expression level or to produce a Cas protein from an exogenously introduced nucleic acid, which nucleic acid encodes a Cas that is same or different from the endogenous Cas. In some case, the cell does not naturally produce Cas protein and is genetically engineered to produce a Cas protein. The Cas protein is deployed in mammalian cells (and putatively within plant cells) by co-expressing the Cas nuclease with guide RNA. Two forms of guide RNAs can be used to facilitate Cas-mediated genome cleavage as disclosed in Le Cong, F., et al., (2013) Science 339(6121):819-823.

In other embodiments, the DNA-binding domain may be associated with a cleavage (nuclease) domain. For example, homing endonucleases may be modified in their DNA-binding specificity while retaining nuclease function. In addition, zinc finger proteins may also be fused to a cleavage domain to form a zinc finger nuclease (ZFN). The cleavage domain portion of the fusion proteins disclosed herein can be obtained from any endonuclease or exonuclease. Exemplary endonucleases from which a cleavage domain can be derived include, but are not limited to, restriction endonucleases and homing endonucleases. See, for example, 2002-2003 Catalogue, New England Biolabs, Beverly, Mass.; and Belfort et al. (1997) Nucleic Acids Res. 25:3379-3388. Additional enzymes which cleave DNA are known (e.g., 51 Nuclease; mung bean nuclease; pancreatic DNase I; micrococcal nuclease; yeast HO endonuclease; see also Linn et al. (eds.) Nucleases, Cold Spring Harbor Laboratory Press, 1993). Non limiting examples of homing endonucleases and meganucleases include I-SceI, I-CeuI, PI-PspI, PI-Sce, I-SceIV, I-CsmI, I-PanI, I-SceII, I-PpoI, I-SceIII, I-CreI, I-TevI, I-TevII and I-TevIII are known. See also U.S. Pat. Nos. 5,420,032; 6,833,252; Belfort et al. (1997) Nucleic Acids Res. 25:3379-3388; Dujon et al. (1989) Gene 82:115-118; Perler et al. (1994) Nucleic Acids Res. 22, 1125-1127; Jasin (1996) Trends Genet. 12:224-228; Gimble et al. (1996) J. Mol. Biol. 263:163-180; Argast et al. (1998) J. Mol. Biol. 280:345-353 and the New England Biolabs catalogue. One or more of these enzymes (or functional fragments thereof) can be used as a source of cleavage domains and cleavage half-domains.

Restriction endonucleases (restriction enzymes) are present in many species and are capable of sequence-specific binding to DNA (at a recognition site), and cleaving DNA at or near the site of binding. Certain restriction enzymes (e.g., Type IIS) cleave DNA at sites removed from the recognition site and have separable binding and cleavage domains. For example, the Type IIS enzyme FokI catalyzes double-stranded cleavage of DNA, at 9 nucleotides from its recognition site on one strand and 13 nucleotides from its recognition site on the other. See, for example, U.S. Pat. Nos. 5,356,802; 5,436,150 and 5,487,994; as well as Li et al. (1992) Proc. Natl. Acad. Sci. USA 89:4275-4279; Li et al. (1993) Proc. Natl. Acad. Sci. USA 90:2764-2768; Kim et al. (1994a) Proc. Natl. Acad. Sci. USA 91:883-887; Kim et al. (1994b) J. Biol. Chem. 269:31,978-31,982. Thus, in one embodiment, fusion proteins comprise the cleavage domain (or cleavage half-domain) from at least one Type IIS restriction enzyme and one or more zinc finger binding domains, which may or may not be engineered.

An exemplary Type IIS restriction enzyme, whose cleavage domain is separable from the binding domain, is FokI. This particular enzyme is active as a dimer. Bitinaite et al. (1998) Proc. Natl. Acad. Sci. USA 95: 10,570-10,575. Accordingly, for the purposes of the present disclosure, the portion of the FokI enzyme used in the disclosed fusion proteins is considered a cleavage half-domain. Thus, for targeted double-stranded cleavage and/or targeted replacement of cellular sequences using zinc finger-FokI fusions, two fusion proteins, each comprising a FokI cleavage half-domain, can be used to reconstitute a catalytically active cleavage domain. Alternatively, a single polypeptide molecule containing a zinc finger binding domain and two FokI cleavage half-domains can also be used. Parameters for targeted cleavage and targeted sequence alteration using zinc finger-FokI fusions are provided elsewhere in this disclosure.

A cleavage domain or cleavage half-domain can be any portion of a protein that retains cleavage activity, or that retains the ability to multimerize (e.g., dimerize) to form a functional cleavage domain. Exemplary Type IIS restriction enzymes are described in International Publication WO 2007/014275, incorporated by reference herein in its entirety.

To enhance cleavage specificity, cleavage domains may also be modified. In certain embodiments, variants of the cleavage half-domain are employed these variants minimize or prevent homodimerization of the cleavage half-domains. Non-limiting examples of such modified cleavage half-domains are described in detail in WO 2007/014275, incorporated by reference in its entirety herein. In certain embodiments, the cleavage domain comprises an engineered cleavage half-domain (also referred to as dimerization domain mutants) that minimize or prevent homodimerization. Such embodiments are known to those of skill the art and described for example in U.S. Patent Publication Nos. 20050064474; 20060188987; 20070305346 and 20080131962, the disclosures of all of which are incorporated by reference in their entireties herein. Amino acid residues at positions 446, 447, 479, 483, 484, 486, 487, 490, 491, 496, 498, 499, 500, 531, 534, 537, and 538 of FokI are all targets for influencing dimerization of the FokI cleavage half-domains.

Additional engineered cleavage half-domains of FokI that form obligate heterodimers can also be used in the ZFNs described herein. Exemplary engineered cleavage half-domains of Fok I that form obligate heterodimers include a pair in which a first cleavage half-domain includes mutations at amino acid residues at positions 490 and 538 of Fok I and a second cleavage half-domain includes mutations at amino acid residues 486 and 499. In one embodiment, a mutation at 490 replaces Glu (E) with Lys (K); the mutation at 538 replaces Iso (I) with Lys (K); the mutation at 486 replaced Gln (Q) with Glu (E); and the mutation at position 499 replaces Iso (I) with Lys (K). Specifically, the engineered cleavage half-domains described herein were prepared by mutating positions 490 (E→K) and 538 (I→K) in one cleavage half-domain to produce an engineered cleavage half-domain designated “E490K:I538K” and by mutating positions 486 (Q→E) and 499 (I→L) in another cleavage half-domain to produce an engineered cleavage half-domain designated “Q486E:I499L”. The engineered cleavage half-domains described herein are obligate heterodimer mutants in which aberrant cleavage is minimized or abolished. See, e.g., U.S. Patent Publication No. 2008/0131962, the disclosure of which is incorporated by reference in its entirety for all purposes. In certain embodiments, the engineered cleavage half-domain comprises mutations at positions 486, 499 and 496 (numbered relative to wild-type FokI), for instance mutations that replace the wild type Gln (Q) residue at position 486 with a Glu (E) residue, the wild type Iso (I) residue at position 499 with a Leu (L) residue and the wild-type Asn (N) residue at position 496 with an Asp (D) or Glu (E) residue (also referred to as a “ELD” and “ELE” domains, respectively). In other embodiments, the engineered cleavage half-domain comprises mutations at positions 490, 538 and 537 (numbered relative to wild-type FokI), for instance mutations that replace the wild type Glu (E) residue at position 490 with a Lys (K) residue, the wild type Iso (I) residue at position 538 with a Lys (K) residue, and the wild-type His (H) residue at position 537 with a Lys (K) residue or a Arg (R) residue (also referred to as “KKK” and “KKR” domains, respectively). In other embodiments, the engineered cleavage half-domain comprises mutations at positions 490 and 537 (numbered relative to wild-type FokI), for instance mutations that replace the wild type Glu (E) residue at position 490 with a Lys (K) residue and the wild-type His (H) residue at position 537 with a Lys (K) residue or a Arg (R) residue (also referred to as “KIK” and “KIR” domains, respectively). (See US Patent Publication No. 20110201055). In other embodiments, the engineered cleavage half domain comprises the “Sharkey” and/or “Sharkey′” mutations (see Guo et al, (2010) J. Mol. Biol. 400(1):96-107).

Engineered cleavage half-domains described herein can be prepared using any suitable method, for example, by site-directed mutagenesis of wild-type cleavage half-domains (Fok I) as described in U.S. Patent Publication Nos. 20050064474; 20080131962; and 20110201055. Alternatively, nucleases may be assembled in vivo at the nucleic acid target site using so-called “split-enzyme” technology (see e.g. U.S. Patent Publication No. 20090068164). Components of such split enzymes may be expressed either on separate expression constructs, or can be linked in one open reading frame where the individual components are separated, for example, by a self-cleaving 2A peptide or IRES sequence. Components may be individual zinc finger binding domains or domains of a meganuclease nucleic acid binding domain.

Nucleases can be screened for activity prior to use, for example in a yeast-based chromosomal system as described in WO 2009/042163 and 20090068164. Nuclease expression constructs can be readily designed using methods known in the art. See, e.g., United States Patent Publications 20030232410; 20050208489; 20050026157; 20050064474; 20060188987; 20060063231; and International Publication WO 07/014275. Expression of the nuclease may be under the control of a constitutive promoter or an inducible promoter, for example the galactokinase promoter which is activated (de-repressed) in the presence of raffinose and/or galactose and repressed in presence of glucose.

Distance between target sites refers to the number of nucleotides or nucleotide pairs intervening between two target sites as measured from the edges of the sequences nearest each other. In certain embodiments in which cleavage depends on the binding of two zinc finger domain/cleavage half-domain fusion molecules to separate target sites, the two target sites can be on opposite DNA strands. In other embodiments, both target sites are on the same DNA strand. For targeted integration into the optimal genomic locus, one or more ZFPs are engineered to bind a target site at or near the predetermined cleavage site, and a fusion protein comprising the engineered DNA-binding domain and a cleavage domain is expressed in the cell. Upon binding of the zinc finger portion of the fusion protein to the target site, the DNA is cleaved, preferably via a double-stranded break, near the target site by the cleavage domain.

The presence of a double-stranded break in the optimal genomic locus facilitates integration of exogenous sequences via homologous recombination. Thus, in one embodiment the polynucleotide comprising the nucleic acid sequence of interest to be inserted into the targeted genomic locus will include one or more regions of homology with the targeted genomic locus to facilitate homologous recombination.

In addition to the fusion molecules described herein, targeted replacement of a selected genomic sequence also involves the introduction of a donor sequence. The polynucleotide donor sequence can be introduced into the cell prior to, concurrently with, or subsequent to, expression of the fusion protein(s). In one embodiment the donor polynucleotide contains sufficient homology to the optimal genomic locus to support homologous recombination between it and the optimal genomic locus genomic sequence to which it bears homology. Approximately 25, 50, 100, 200, 500, 750, 1,000, 1,500, 2,000 nucleotides or more of sequence homology between a donor and a genomic sequence, or any integral value between 10 and 2,000 nucleotides or more, will support homologous recombination. In certain embodiments, the homology arms are less than 1,000 basepairs in length. In other embodiments, the homology arms are less than 750 base pairs in length. In one embodiment, donor polynucleotide sequences can comprise a vector molecule containing sequences that are not homologous to the region of interest in cellular chromatin. A donor polynucleotide molecule can contain several, discontinuous regions of homology to cellular chromatin. For example, for targeted insertion of sequences not normally present in a region of interest, said sequences can be present in a donor nucleic acid molecule and flanked by regions of homology to sequence in the region of interest. The donor polynucleotide can be DNA or RNA, single-stranded or double-stranded and can be introduced into a cell in linear or circular form. See, e.g., U.S. Patent Publication Nos. 20100047805, 20110281361, 20110207221 and U.S. application Ser. No. 13/889,162. If introduced in linear form, the ends of the donor sequence can be protected (e.g., from exonucleolytic degradation) by methods known to those of skill in the art. For example, one or more dideoxynucleotide residues are added to the 3′ terminus of a linear molecule and/or self-complementary oligonucleotides are ligated to one or both ends. See, for example, Chang et al. (1987) Proc. Natl. Acad. Sci. USA 84:4959-4963; Nehls et al. (1996) Science 272:886-889. Additional methods for protecting exogenous polynucleotides from degradation include, but are not limited to, addition of terminal amino group(s) and the use of modified internucleotide linkages such as, for example, phosphorothioates, phosphoramidates, and O-methyl ribose or deoxyribose residues.

In accordance with one embodiment a method of preparing a transgenic maize plant is provided wherein a DNA of interest has been inserted into an optimal nongenic maize genomic locus. The method comprises the steps of:

a. selecting an optimal nongenic maize locus as a target for insertion of the nucleic acid of interest;

b. introducing a site specific nuclease into a maize plant cell, wherein the site specific nuclease cleaves the nongenic sequence;

c. introducing the DNA of interest into the plant cell; and

d. selecting transgenic plant cells comprising the DNA of interest targeted to said nongenic sequence.

In accordance with one embodiment a method of preparing a transgenic maize protoplast cell is provided wherein a DNA of interest has been inserted into an optimal nongenic maize genomic locus. The method comprises the steps of:

a. selecting an optimal nongenic maize locus as a target for insertion of the nucleic acid of interest;

b. introducing a site specific nuclease into a maize protoplast cell, wherein the site specific nuclease cleaves the nongenic sequence;

c. introducing the DNA of interest into the maize protoplast cell; and

d. selecting the transgenic maize protoplast cell comprising the DNA of interest targeted to said nongenic sequence.

In one embodiment the site specific nuclease is selected from the group consisting of a Zinc Finger nuclease, a CRISPR nuclease, a TALEN nuclease, or a meganuclease, and more particularly in one embodiment the site specific nuclease is a Zinc Finger nuclease. In accordance with one embodiment the DNA of interest is integrated within said nongenic sequence via a homology directed repair integration method. Alternatively, in some embodiments the DNA of interest is integrated within said nongenic sequence via a non-homologous end joining integration method. In additional embodiments, the DNA of interest is integrated within said nongenic sequence via a previously undescribed integration method. In one embodiment the method comprises selecting a optimal nongenic maize genomic locus for targeted insertion of a DNA of interest that has 2, 3, 4, 5, 6, 7, or 8 of the following characteristics:

a. the nongenic sequence is at least 1 Kb in length and does not contain greater than 1% DNA methylation within the sequence;

b. the nongenic sequence exhibits a 0.00041 to 62.42 cM/Mb rate of recombination within the maize genome;

c. the nongenic sequence exhibits a 0 to 0.962 level of nucleosome occupancy of the maize genome;

d. the nongenic sequence shares less than 40% sequence identity with any other sequence contained in the maize genome;

e. the nongenic sequence has a relative location value from 0.00373 to 0.99908 ratio of genomic distance from a maize chromosomal centromere;

f. the nongenic sequence has a guanine/cytosine percent content range of 25.17 to 68.3%;

g. the nongenic sequence is located proximally to a genic sequence; and,

h. a 1 Mb region of maize genomic sequence comprising said nongenic sequence comprises one or more additional nongenic sequences. In one embodiment the optimal nongenic maize locus is selected from a loci of cluster 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31 or 32.

Delivery

The donor molecules disclosed herein are integrated into a genome of a cell via targeted, homology-independent and/or homology-dependent methods. For such targeted integration, the genome is cleaved at a desired location (or locations) using a nuclease, for example, a fusion between a DNA-binding domain (e.g., zinc finger binding domain, CRISPR or TAL effector domain is engineered to bind a target site at or near the predetermined cleavage site) and nuclease domain (e.g., cleavage domain or cleavage half-domain). In certain embodiments, two fusion proteins, each comprising a DNA-binding domain and a cleavage half-domain, are expressed in a cell, and bind to target sites which are juxtaposed in such a way that a functional cleavage domain is reconstituted and DNA is cleaved in the vicinity of the target sites. In one embodiment, cleavage occurs between the target sites of the two DNA-binding domains. One or both of the DNA-binding domains can be engineered. See, also, U.S. Pat. No. 7,888,121; U.S. Patent Publication 20050064474 and International Patent Publications WO05/084190, WO05/014791 and WO 03/080809.

The nucleases as described herein can be introduced as polypeptides and/or polynucleotides. For example, two polynucleotides, each comprising sequences encoding one of the aforementioned polypeptides, can be introduced into a cell, and when the polypeptides are expressed and each binds to its target sequence, cleavage occurs at or near the target sequence. Alternatively, a single polynucleotide comprising sequences encoding both fusion polypeptides is introduced into a cell. Polynucleotides can be DNA, RNA or any modified forms or analogues or DNA and/or RNA.

Following the introduction of a double-stranded break in the region of interest, the transgene is integrated into the region of interest in a targeted manner via non-homology dependent methods (e.g., non-homologous end joining (NHEJ)) following linearization of a double-stranded donor molecule as described herein. The double-stranded donor is preferably linearized in vivo with a nuclease, for example one or more of the same or different nucleases that are used to introduce the double-stranded break in the genome. Synchronized cleavage of the chromosome and the donor in the cell may limit donor DNA degradation (as compared to linearization of the donor molecule prior to introduction into the cell). The nuclease target sites used for linearization of the donor preferably do not disrupt the transgene(s) sequence(s).

The transgene may be integrated into the genome in the direction expected by simple ligation of the nuclease overhangs (designated “forward” or “AB” orientation) or in the alternate direction (designated “reverse” or “BA” orientation). In certain embodiments, the transgene is integrated following accurate ligation of the donor and chromosome overhangs. In other embodiments, integration of the transgene in either the BA or AB orientation results in deletion of several nucleotides.

Through the application of techniques such as these, the cells of virtually any species may be stably transformed. In some embodiments, transforming DNA is integrated into the genome of the host cell. In the case of multicellular species, transgenic cells may be regenerated into a transgenic organism. Any of these techniques may be used to produce a transgenic plant, for example, comprising one or more donor polynucleotide acid sequences in the genome of the transgenic plant.

The delivery of nucleic acids may be introduced into a plant cell in embodiments of the invention by any method known to those of skill in the art, including, for example and without limitation: by transformation of protoplasts (See, e.g., U.S. Pat. No. 5,508,184); by desiccation/inhibition-mediated DNA uptake (See, e.g., Potrykus et al. (1985) Mol. Gen. Genet. 199:183-8); by electroporation (See, e.g., U.S. Pat. No. 5,384,253); by agitation with silicon carbide fibers (See, e.g., U.S. Pat. Nos. 5,302,523 and 5,464,765); by Agrobacterium-mediated transformation (See, e.g., U.S. Pat. Nos. 5,563,055, 5,591,616, 5,693,512, 5,824,877, 5,981,840, and 6,384,301); by acceleration of DNA-coated particles (See, e.g., U.S. Pat. Nos. 5,015,580, 5,550,318, 5,538,880, 6,160,208, 6,399,861, and 6,403,865) and by Nanoparticles, nanocarriers and cell penetrating peptides (WO201126644A2; WO2009046384A1; WO2008148223A1) in the methods to deliver DNA, RNA, Peptides and/or proteins or combinations of nucleic acids and peptides into plant cells.

The most widely-utilized method for introducing an expression vector into plants is based on the natural transformation system of Agrobacterium. A. tumefaciens and A. rhizogenes are plant pathogenic soil bacteria that genetically transform plant cells. The T_(i) and R_(i) plasmids of A. tumefaciens and A. rhizogenes, respectively, carry genes responsible for genetic transformation of the plant. The T_(i) (tumor-inducing)-plasmids contain a large segment, known as T-DNA, which is transferred to transformed plants. Another segment of the T_(i) plasmid, the vir region, is responsible for T-DNA transfer. The T-DNA region is bordered by left-hand and right-hand borders that are each composed of terminal repeated nucleotide sequences. In some modified binary vectors, the tumor-inducing genes have been deleted, and the functions of the vir region are utilized to transfer foreign DNA bordered by the T-DNA border sequences. The T-region may also contain, for example, a selectable marker for efficient recovery of transgenic plants and cells, and a multiple cloning site for inserting sequences for transfer such as a nucleic acid encoding a fusion protein of the invention.

Thus, in some embodiments, a plant transformation vector is derived from a T_(i) plasmid of A. tumefaciens (See, e.g., U.S. Pat. Nos. 4,536,475, 4,693,977, 4,886,937, and 5,501,967; and European Patent EP 0 122 791) or a R, plasmid of A. rhizogenes. Additional plant transformation vectors include, for example and without limitation, those described by Herrera-Estrella et al. (1983) Nature 303:209-13; Bevan et al. (1983), supra; Klee et al. (1985) Bio/Technol. 3:637-42; and in European Patent EP 0 120 516, and those derived from any of the foregoing. Other bacteria, such as Sinorhizobium, Rhizobium, and Mesorhizobium, that naturally interact with plants can be modified to mediate gene transfer to a number of diverse plants. These plant-associated symbiotic bacteria can be made competent for gene transfer by acquisition of both a disarmed T_(i) plasmid and a suitable binary vector.

The Nucleic Acid of Interest

The polynucleotide donor sequences for targeted insertion into a maize genomic locus typically range in length from about 10 to about 5,000 nucleotides. However, nucleotides substantially longer, up to 20,000 nucleotides can be used, including sequences of about 5, 6, 7, 8, 9, 10, 11 and 12 Kb in length. Additionally, donor sequences can comprise a vector molecule containing sequences that are not homologous to the replaced region. In one embodiment the nucleic acid of interest will include one or more regions that share homology with the targeted genomic loci. Generally, the homologous region(s) of the nucleic acid sequence of interest will have at least 50% sequence identity to a genomic sequence with which recombination is desired. In certain embodiments, the homologous region(s) of the nucleic acid of interest shares 60%, 70%, 80%, 90%, 95%, 98%, 99%, or 99.9% sequence identity with sequences located in the targeted genomic locus. However, any value between 1% and 100% sequence identity can be present, depending upon the length of the nucleic acid of interest.

A nucleic acid of interest can contain several, discontinuous regions of sequence sharing relatively high sequence identity to cellular chromatin. For example, for targeted insertion of sequences not normally present in a targeted genomic locus, the unique sequences can be present in a donor nucleic acid molecule and flanked by regions of sequences that share a relatively high sequence identity to a sequence present in the targeted genomic locus.

A nucleic acid of interest can also be inserted into a targeted genomic locus to serve as a reservoir for later use. For example, a first nucleic acid sequence comprising sequences homologous to a nongenic region of the maize genome, but containing a nucleic acid of interest (optionally encoding a ZFN under the control of an inducible promoter), may be inserted in a targeted genomic locus. Next, a second nucleic acid sequence is introduced into the cell to induce the insertion of a DNA of interest into an optimal nongenic maize genomic locus. Either the first nucleic acid sequence comprises a ZFNs specific to the optimal nongenic maize genomic locus and the second nucleic acid sequence comprises the DNA sequence of interest, or vice versa. In one embodiment the ZFN will cleave both the optimal nongenic maize genomic locus and the nucleic acid of interest. The resulting double stranded break in the genome can then become the integration site for the nucleic acid of interest released from the optimal genomic locus. Alternatively, expression of a ZFN already located in the genome can be induced after introduction of the DNA of interest to induce a double stranded break in the genome that can then become the integration site for the introduced nucleic acid of interest. In this way, the efficiency of targeted integration of a DNA of interest at any region of interest may be improved since the method does not rely on simultaneous uptake of both the nucleic acids encoding the ZFNs and the DNA of interest.

A nucleic acid of interest can also be inserted into an optimal nongenic maize genomic locus to serve as a target site for subsequent insertions. For example, a nucleic acid of interest comprised of DNA sequences that contain recognition sites for additional ZFN designs may be inserted into the locus. Subsequently, additional ZFN designs may be generated and expressed in cells such that the original nucleic acid of interest is cleaved and modified by repair or homologous recombination. In this way, reiterative integrations of nucleic acid of interests may occur at the optimal nongenic maize genomic locus.

Exemplary exogenous sequences that can be inserted into an optimal nongenic maize genomic locus include, but are not limited to, any polypeptide coding sequence (e.g., cDNAs), promoter, enhancer and other regulatory sequences (e.g., interfering RNA sequences, shRNA expression cassettes, epitope tags, marker genes, cleavage enzyme recognition sites and various types of expression constructs. Such sequences can be readily obtained using standard molecular biological techniques (cloning, synthesis, etc.) and/or are commercially available.

To express ZFNs, sequences encoding the fusion proteins are typically subcloned into an expression vector that contains a promoter to direct transcription. Suitable prokaryotic and eukaryotic promoters are well known in the art and described, e.g., in Sambrook et al., Molecular Cloning, A Laboratory Manual (2nd ed. 1989; 3.sup.rd ed., 2001); Kriegler, Gene Transfer and Expression: A Laboratory Manual (1990); and Current Protocols in Molecular Biology (Ausubel et al., supra. Bacterial expression systems for expressing the ZFNs are available in, e.g., E. coli, Bacillus sp., and Salmonella (Palva et al., Gene 22:229-235 (1983)). Kits for such expression systems are commercially available. Eukaryotic expression systems for mammalian cells, yeast, and insect cells are well known by those of skill in the art and are also commercially available.

The particular expression vector used to transport the genetic material into the cell is selected with regard to the intended use of the fusion proteins, e.g., expression in plants, animals, bacteria, fungus, protozoa, etc. (see expression vectors described below). Standard bacterial and animal expression vectors are known in the art and are described in detail, for example, U.S. Patent Publication 20050064474A1 and International Patent Publications WO05/084190, WO05/014791 and WO03/080809.

Standard transfection methods can be used to produce bacterial, mammalian, yeast or insect cell lines that express large quantities of protein, which can then be purified using standard techniques (see, e.g., Colley et al., J. Biol. Chem. 264:17619-17622 (1989); Guide to Protein Purification, in Methods in Enzymology, vol. 182 (Deutscher, ed., 1990)). Transformation of eukaryotic and prokaryotic cells are performed according to standard techniques (see, e.g., Morrison, J. Bact. 132:349-351 (1977); Clark-Curtiss & Curtiss, Methods in Enzymology 101:347-362 (Wu et al., eds., 1983).

The disclosed methods and compositions can be used to insert polynucleotide donor sequences into a predetermined location such as one of the optimal nongenic maize genomic loci. This is useful inasmuch as expression of an introduced transgene into the maize genome depends critically on its integration site. Accordingly, genes encoding herbicide tolerance, insect resistance, nutrients, antibiotics or therapeutic molecules can be inserted, by targeted recombination.

In one embodiment the nucleic acid of interest is combined or “stacked” with gene encoding sequences that provide additional resistance or tolerance to glyphosate or another herbicide, and/or provides resistance to select insects or diseases and/or nutritional enhancements, and/or improved agronomic characteristics, and/or proteins or other products useful in feed, food, industrial, pharmaceutical or other uses. The “stacking” of two or more nucleic acid sequences of interest within a plant genome can be accomplished, for example, via conventional plant breeding using two or more events, transformation of a plant with a construct which contains the sequences of interest, re-transformation of a transgenic plant, or addition of new traits through targeted integration via homologous recombination.

Such polynucleotide donor nucleotide sequences of interest include, but are not limited to, those examples provided below:

1. Genes or Coding Sequence (e.g. iRNA) that Confer Resistance to Pests or Disease

(A) Plant Disease Resistance Genes. Plant defenses are often activated by specific interaction between the product of a disease resistance gene (R) in the plant and the product of a corresponding avirulence (Avr) gene in the pathogen. A plant variety can be transformed with cloned resistance gene to engineer plants that are resistant to specific pathogen strains. Examples of such genes include, the tomato Cf-9 gene for resistance to Cladosporium fulvum (Jones et al., 1994 Science 266:789), tomato Pto gene, which encodes a protein kinase, for resistance to Pseudomonas syringae pv. tomato (Martin et al., 1993 Science 262:1432), and Arabidopsis RSSP2 gene for resistance to Pseudomonas syringae (Mindrinos et al., 1994 Cell 78:1089).

(B) A Bacillus thuringiensis protein, a derivative thereof or a synthetic polypeptide modeled thereon, such as, a nucleotide sequence of a Bt δ-endotoxin gene (Geiser et al., 1986 Gene 48:109), and a vegetative insecticidal (VIP) gene (see, e.g., Estruch et al. (1996) Proc. Natl. Acad. Sci. 93:5389-94). Moreover, DNA molecules encoding δ-endotoxin genes can be purchased from American Type Culture Collection (Rockville, Md.), under ATCC accession numbers 40098, 67136, 31995 and 31998.

(C) A lectin, such as, nucleotide sequences of several Clivia miniata mannose-binding lectin genes (Van Damme et al., 1994 Plant Molec. Biol. 24:825).

(D) A vitamin binding protein, such as avidin and avidin homologs which are useful as larvicides against insect pests. See U.S. Pat. No. 5,659,026.

(E) An enzyme inhibitor, e.g., a protease inhibitor or an amylase inhibitor. Examples of such genes include a rice cysteine proteinase inhibitor (Abe et al., 1987 J. Biol. Chem. 262:16793), a tobacco proteinase inhibitor I (Huub et al., 1993 Plant Molec. Biol. 21:985), and an α-amylase inhibitor (Sumitani et al., 1993 Biosci. Biotech. Biochem. 57:1243).

(F) An insect-specific hormone or pheromone such as an ecdysteroid and juvenile hormone a variant thereof, a mimetic based thereon, or an antagonist or agonist thereof, such as baculovirus expression of cloned juvenile hormone esterase, an inactivator of juvenile hormone (Hammock et al., 1990 Nature 344:458).

(G) An insect-specific peptide or neuropeptide which, upon expression, disrupts the physiology of the affected pest (J. Biol. Chem. 269:9). Examples of such genes include an insect diuretic hormone receptor (Regan, 1994), an allostatin identified in Diploptera punctata (Pratt, 1989), and insect-specific, paralytic neurotoxins (U.S. Pat. No. 5,266,361).

(H) An insect-specific venom produced in nature by a snake, a wasp, etc., such as a scorpion insectotoxic peptide (Pang, 1992 Gene 116:165).

(I) An enzyme responsible for a hyperaccumulation of monoterpene, a sesquiterpene, a steroid, hydroxamic acid, a phenylpropanoid derivative or another non-protein molecule with insecticidal activity.

(J) An enzyme involved in the modification, including the post-translational modification, of a biologically active molecule; for example, glycolytic enzyme, a proteolytic enzyme, a lipolytic enzyme, a nuclease, a cyclase, a transaminase, an esterase, a hydrolase, a phosphatase, a kinase, a phosphorylase, a polymerase, an elastase, a chitinase and a glucanase, whether natural or synthetic. Examples of such genes include, a callas gene (PCT published application WO93/02197), chitinase-encoding sequences (which can be obtained, for example, from the ATCC under accession numbers 3999637 and 67152), tobacco hookworm chitinase (Kramer et al., 1993 Insect Molec. Biol. 23:691), and parsley ubi4-2 polyubiquitin gene (Kawalleck et al., 1993 Plant Molec. Biol. 21:673).

(K) A molecule that stimulates signal transduction. Examples of such molecules include nucleotide sequences for mung bean calmodulin cDNA clones (Botella et al., 1994 Plant Molec. Biol. 24:757) and a nucleotide sequence of a maize calmodulin cDNA clone (Griess et al., 1994 Plant Physiol. 104:1467).

(L) A hydrophobic moment peptide. See U.S. Pat. Nos. 5,659,026 and 5,607,914; the latter teaches synthetic antimicrobial peptides that confer disease resistance.

(M) A membrane permease, a channel former or a channel blocker, such as a cecropin-β lytic peptide analog (Jaynes et al., 1993 Plant Sci. 89:43) which renders transgenic tobacco plants resistant to Pseudomonas solanacearum.

(N) A viral-invasive protein or a complex toxin derived therefrom. For example, the accumulation of viral coat proteins in transformed plant cells imparts resistance to viral infection and/or disease development effected by the virus from which the coat protein gene is derived, as well as by related viruses. Coat protein-mediated resistance has been conferred upon transformed plants against alfalfa mosaic virus, cucumber mosaic virus, tobacco streak virus, potato virus X, potato virus Y, tobacco etch virus, tobacco rattle virus and tobacco mosaic virus. See, for example, Beachy et al. (1990) Ann. Rev. Phytopathol. 28:451.

(o) An insect-specific antibody or an immunotoxin derived therefrom. Thus, an antibody targeted to a critical metabolic function in the insect gut would inactivate an affected enzyme, killing the insect. For example, Taylor et al. (1994) Abstract #497, Seventh Int'l. Symposium on Molecular Plant-Microbe Interactions shows enzymatic inactivation in transgenic tobacco via production of single-chain antibody fragments.

(P) A virus-specific antibody. See, for example, Tavladoraki et al. (1993) Nature 266:469, which shows that transgenic plants expressing recombinant antibody genes are protected from virus attack.

(Q) A developmental-arrestive protein produced in nature by a pathogen or a parasite. Thus, fungal endo α-1,4-D polygalacturonases facilitate fungal colonization and plant nutrient release by solubilizing plant cell wall homo-α-1,4-D-galacturonase (Lamb et al., 1992) Bio/Technology 10:1436. The cloning and characterization of a gene which encodes a bean endopolygalacturonase-inhibiting protein is described by Toubart et al. (1992 Plant J. 2:367).

(R) A developmental-arrestive protein produced in nature by a plant, such as the barley ribosome-inactivating gene that provides an increased resistance to fungal disease (Longemann et al., 1992). Bio/Technology 10:3305.

(S) RNA interference, in which an RNA molecule is used to inhibit expression of a target gene. An RNA molecule in one example is partially or fully double stranded, which triggers a silencing response, resulting in cleavage of dsRNA into small interfering RNAs, which are then incorporated into a targeting complex that destroys homologous mRNAs. See, e.g., Fire et al., U.S. Pat. No. 6,506,559; Graham et al. U.S. Pat. No. 6,573,099.

2. Genes that Confer Resistance to a Herbicide

(A) Genes encoding resistance or tolerance to a herbicide that inhibits the growing point or meristem, such as an imidazalinone, sulfonanilide or sulfonylurea herbicide. Exemplary genes in this category code for mutant acetolactate synthase (ALS) (Lee et al., 1988 EMBOJ. 7:1241) also known as acetohydroxyacid synthase (AHAS) enzyme (Miki et al., 1990 Theor. Appl. Genet. 80:449).

(B) One or more additional genes encoding resistance or tolerance to glyphosate imparted by mutant EPSP synthase and aroA genes, or through metabolic inactivation by genes such as DGT-28, 2mEPSPS, GAT (glyphosate acetyltransferase) or GOX (glyphosate oxidase) and other phosphono compounds such as glufosinate (pat, bar, and dsm-2 genes), and aryloxyphenoxypropionic acids and cyclohexanediones (ACCase inhibitor encoding genes). See, for example, U.S. Pat. No. 4,940,835, which discloses the nucleotide sequence of a form of EPSP which can confer glyphosate resistance. A DNA molecule encoding a mutant aroA gene can be obtained under ATCC Accession Number 39256, and the nucleotide sequence of the mutant gene is disclosed in U.S. Pat. No. 4,769,061. European patent application No. 0 333 033 and U.S. Pat. No. 4,975,374 disclose nucleotide sequences of glutamine synthetase genes which confer resistance to herbicides such as L-phosphinothricin. The nucleotide sequence of a phosphinothricinacetyl-transferase gene is provided in European application No. 0 242 246. De Greef et al. (1989) Bio/Technology 7:61 describes the production of transgenic plants that express chimeric bar genes coding for phosphinothricin acetyl transferase activity. Exemplary of genes conferring resistance to aryloxyphenoxypropionic acids and cyclohexanediones, such as sethoxydim and haloxyfop, are the Accl-S1, Accl-S2 and Accl-S3 genes described by Marshall et al. (1992) Theor. Appl. Genet. 83:435.

(C) Genes encoding resistance or tolerance to a herbicide that inhibits photosynthesis, such as a triazine (psbA and gs+ genes) and a benzonitrile (nitrilase gene). Przibilla et al. (1991) Plant Cell 3:169 describe the use of plasmids encoding mutant psbA genes to transform Chlamydomonas. Nucleotide sequences for nitrilase genes are disclosed in U.S. Pat. No. 4,810,648, and DNA molecules containing these genes are available under ATCC accession numbers 53435, 67441 and 67442. Cloning and expression of DNA coding for a glutathione 5-transferase is described by Hayes et al. (1992) Biochem. J. 285:173.

(D) Genes encoding resistance or tolerance to a herbicide that bind to hydroxyphenylpyruvate dioxygenases (HPPD), enzymes which catalyze the reaction in which para-hydroxyphenylpyruvate (HPP) is transformed into homogentisate. This includes herbicides such as isoxazoles (EP418175, EP470856, EP487352, EP527036, EP560482, EP682659, U.S. Pat. No. 5,424,276), in particular isoxaflutole, which is a selective herbicide for maize, diketonitriles (EP496630, EP496631), in particular 2-cyano-3-cyclopropyl-1-(2-SO2CH3-4-CF3 phenyl)propane-1,3-dione and 2-cyano-3-cyclopropyl-1-(2-SO2CH3-4-2,3Cl2phenyl)propane-1,3-dione, triketones (EP625505, EP625508, U.S. Pat. No. 5,506,195), in particular sulcotrione, and pyrazolinates. A gene that produces an overabundance of HPPD in plants can provide tolerance or resistance to such herbicides, including, for example, genes described in U.S. Pat. Nos. 6,268,549 and 6,245,968 and U.S. Patent Application, Publication No. 20030066102.

(E) Genes encoding resistance or tolerance to phenoxy auxin herbicides, such as 2,4-dichlorophenoxyacetic acid (2,4-D) and which may also confer resistance or tolerance to aryloxyphenoxypropionate (AOPP) herbicides. Examples of such genes include the α-ketoglutarate-dependent dioxygenase enzyme (aad-1) gene, described in U.S. Pat. No. 7,838,733.

(F) Genes encoding resistance or tolerance to phenoxy auxin herbicides, such as 2,4-dichlorophenoxyacetic acid (2,4-D) and which may also confer resistance or tolerance to pyridyloxy auxin herbicides, such as fluroxypyr or triclopyr. Examples of such genes include the α-ketoglutarate-dependent dioxygenase enzyme gene (aad-12), described in WO 2007/053482 A2.

(G) Genes encoding resistance or tolerance to dicamba (see, e.g., U.S. Patent Publication No. 20030135879).

(H) Genes providing resistance or tolerance to herbicides that inhibit protoporphyrinogen oxidase (PPO) (see U.S. Pat. No. 5,767,373).

(I) Genes providing resistance or tolerance to triazine herbicides (such as atrazine) and urea derivatives (such as diuron) herbicides which bind to core proteins of photosystem II reaction centers (PS II) (See Brussian et al., (1989) EMBO J. 1989, 8(4): 1237-1245.

3. Genes that Confer or Contribute to a Value-Added Trait

(A) Modified fatty acid metabolism, for example, by transforming maize or Brassica with an antisense gene or stearoyl-ACP desaturase to increase stearic acid content of the plant (Knultzon et al., 1992) Proc. Nat. Acad. Sci. USA 89:2624.

(B) Decreased Phytate Content

(1) Introduction of a phytase-encoding gene, such as the Aspergillus niger phytase gene (Van Hartingsveldt et al., 1993 Gene 127:87), enhances breakdown of phytate, adding more free phosphate to the transformed plant.

(2) A gene could be introduced that reduces phytate content. In maize, this, for example, could be accomplished by cloning and then reintroducing DNA associated with the single allele which is responsible for maize mutants characterized by low levels of phytic acid (Raboy et al., 1990 Maydica 35:383).

(C) Modified carbohydrate composition effected, for example, by transforming plants with a gene coding for an enzyme that alters the branching pattern of starch. Examples of such enzymes include, Streptococcus mucus fructosyltransferase gene (Shiroza et al., 1988) J. Bacteriol. 170:810, Bacillus subtilis levansucrase gene (Steinmetz et al., 1985 Mol. Gen. Genel. 200:220), Bacillus licheniformis α-amylase (Pen et al., 1992 Bio/Technology 10:292), tomato invertase genes (Elliot et al., 1993), barley amylase gene (Sogaard et al., 1993 J. Biol. Chem. 268:22480), and maize endosperm starch branching enzyme II (Fisher et al., 1993 Plant Physiol. 102:10450).

III. Recombinant Constructs

As disclosed herein the present disclosure provides recombinant genomic sequences comprising an optimal nongenic maize genomic sequence of at least 1 Kb and a DNA of interest, wherein the inserted DNA of interest is inserted into said nongenic sequence. In one embodiment the DNA of interest is an analytical domain, a gene or coding sequence (e.g. iRNA) that confers resistance to pests or disease, genes that confer resistance to a herbicide or genes that confer or contribute to a value-added trait, and the optimal nongenic maize genomic sequence comprises 1, 2, 3, 4, 5, 6, 7, or 8 of the following characteristics:

a. the nongenic sequence is about 1 Kb to about 8.3 Kb in length and does not contain a methylated polynucleotide;

b. the nongenic sequence exhibits a 0.00041 to 62.42 cM/Mb rate of recombination within the maize genome;

c. the nongenic sequence exhibits a 0 to 0.962 level of nucleosome occupancy of the maize genome;

d. the nongenic sequence shares less than 40% sequence identity with any other sequence contained in the maize genome;

e. the nongenic sequence has a relative location value from 0.00373 to 0.99908 ratio of genomic distance from a maize chromosomal centromere;

f. the nongenic sequence has a guanine/cytosine percent content range of 25.17 to 68.3%;

g. the nongenic sequence is located proximally to an genic sequence, comprising a known or predicted maize coding sequence within 40 Kb of contiguous genomic DNA comprising the native nongenic sequence; and,

h. the nongenic sequence is located in a 1 Mb region of maize genomic sequence that comprises at least a second nongenic sequence. In one embodiment the optimal nongenic maize genomic sequence is further characterized as having a genic region comprising 1 to 9 known or predicted maize coding sequence within 40 Kb of contiguous genomic DNA comprising the native nongenic sequence. In one embodiment the optimal nongenic maize locus is selected from a loci of cluster 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31 or 32.

IV. Transgenic Plants

Transgenic plants comprising the recombinant optimal nongenic maize loci are also provided in accordance with one embodiment of the present disclosure. Such transgenic plants can be prepared using techniques known to those skilled in the art.

A transformed maize plant cell, callus, tissue or plant may be identified and isolated by selecting or screening the engineered plant material for traits encoded by the marker genes present on the transforming DNA. For instance, selection can be performed by growing the engineered plant material on media containing an inhibitory amount of the antibiotic or herbicide to which the transforming gene construct confers resistance. Further, transformed cells can also be identified by screening for the activities of any visible marker genes (e.g., the yellow fluorescence protein, green fluorescence protein, red fluorescence protein, beta-glucuronidase, luciferase, B or C1 genes) that may be present on the recombinant nucleic acid constructs. Such selection and screening methodologies are well known to those skilled in the art.

Physical and biochemical methods also may be used to identify plant or plant cell transformants containing inserted gene constructs. These methods include but are not limited to: 1) Southern analysis or PCR amplification for detecting and determining the structure of the recombinant DNA insert; 2) Northern blot, 51 RNase protection, primer-extension or reverse transcriptase-PCR amplification for detecting and examining RNA transcripts of the gene constructs; 3) enzymatic assays for detecting enzyme or ribozyme activity, where such gene products are encoded by the gene construct; 4) protein gel electrophoresis, Western blot techniques, immunoprecipitation, or enzyme-linked immunoassays (ELISA), where the gene construct products are proteins. Additional techniques, such as in situ hybridization, enzyme staining, and immunostaining, also may be used to detect the presence or expression of the recombinant construct in specific plant organs and tissues. The methods for doing all these assays are well known to those skilled in the art.

Effects of gene manipulation using the methods disclosed herein can be observed by, for example, Northern blots of the RNA (e.g., mRNA) isolated from the tissues of interest. Typically, if the mRNA is present or the amount of mRNA has increased, it can be assumed that the corresponding transgene is being expressed. Other methods of measuring gene and/or encoded polypeptide activity can be used. Different types of enzymatic assays can be used, depending on the substrate used and the method of detecting the increase or decrease of a reaction product or by-product. In addition, the levels of polypeptide expressed can be measured immunochemically, i.e., ELISA, RIA, EIA and other antibody based assays well known to those of skill in the art, such as by electrophoretic detection assays (either with staining or western blotting). As one non-limiting example, the detection of the AAD-1 (aryloxyalkanoate dioxygenase; see WO 2005/107437) and PAT (phosphinothricin-N-acetyl-transferase (PAT)) proteins using an ELISA assay is described in U.S. Patent Publication No. 20090093366 which is herein incorporated by reference in its entirety. The transgene may be selectively expressed in some tissues of the plant or at some developmental stages, or the transgene may be expressed in substantially all plant tissues, substantially along its entire life cycle. However, any combinatorial expression mode is also applicable.

One of skill in the art will recognize that after the exogenous polynucleotide donor sequence is stably incorporated in transgenic plants and confirmed to be operable, it can be introduced into other plants by sexual crossing. Any of a number of standard breeding techniques can be used, depending upon the species to be crossed.

The present disclosure also encompasses seeds of the transgenic plants described above wherein the seed has the transgene or gene construct. The present disclosure further encompasses the progeny, clones, cell lines or cells of the transgenic plants described above wherein the progeny, clone, cell line or cell has the transgene or gene construct inserted into an optimal genomic loci.

Transformed plant cells which are produced by any of the above transformation techniques can be cultured to regenerate a whole plant which possesses the transformed genotype and thus the desired phenotype. Such regeneration techniques rely on manipulation of certain phytohormones in a tissue culture growth medium, typically relying on a biocide and/or herbicide marker which has been introduced together with the desired nucleotide sequences. Plant regeneration from cultured protoplasts is described in Evans, et al., “Protoplasts Isolation and Culture” in Handbook of Plant Cell Culture, pp. 124-176, Macmillian Publishing Company, New York, 1983; and Binding, Regeneration of Plants, Plant Protoplasts, pp. 21-73, CRC Press, Boca Raton, 1985. Regeneration can also be obtained from plant callus, explants, organs, pollens, embryos or parts thereof. Such regeneration techniques are described generally in Klee et al. (1987) Ann. Rev. of Plant Phys. 38:467-486.

A transgenic plant or plant material comprising a nucleotide sequence encoding a polypeptide may in some embodiments exhibit one or more of the following characteristics: expression of the polypeptide in a cell of the plant; expression of a portion of the polypeptide in a plastid of a cell of the plant; import of the polypeptide from the cytosol of a cell of the plant into a plastid of the cell; plastid-specific expression of the polypeptide in a cell of the plant; and/or localization of the polypeptide in a cell of the plant. Such a plant may additionally have one or more desirable traits other than expression of the encoded polypeptide. Such traits may include, for example: resistance to insects, other pests, and disease-causing agents; tolerances to herbicides; enhanced stability, yield, or shelf-life; environmental tolerances; pharmaceutical production; industrial product production; and nutritional enhancements.

In accordance with one embodiment a transgenic maize protoplast cell is provided comprising a recombinant optimal nongenic maize locus. More particularly, a maize protoplast plant cell is provided comprising a DNA of interest inserted into an optimal nongenic maize genomic loci of the maize protoplast cell, wherein said nongenic maize genomic loci is about 1 Kb to about 8.3 Kb in length and lacks any methylated nucleotides. In one embodiment the transgenic maize protoplast cell comprises a DNA of interest inserted into the optimal nongenic maize genomic locus wherein the DNA of interest comprises an analytical domain, and/or an open reading frame. In one embodiment the inserted DNA of interest encodes a peptide and in a further embodiment the DNA of interest comprises at least one gene expression cassette comprising a transgene.

In accordance with one embodiment a transgenic maize plant, maize plant part, or maize plant cell is provided comprising a recombinant optimal nongenic maize locus. More particularly, a maize plant, maize plant part, or maize plant cell is provided comprising a DNA of interest inserted into an optimal nongenic maize genomic loci of the maize plant, maize plant part, or maize plant cell, wherein said nongenic maize genomic loci is about 1 Kb to about 8.5 Kb in length and lacks any methylated nucleotides. In one embodiment the transgenic maize plant, maize plant part, or maize plant cell comprises a DNA of interest inserted into the optimal nongenic maize genomic locus wherein the DNA of interest comprises an analytical domain, and/or an open reading frame. In one embodiment the inserted DNA of interest encodes a peptide and in a further embodiment the DNA of interest comprises at least one gene expression cassette comprising a transgene.

In accordance with embodiment 1 a recombinant sequence is provided wherein, said recombinant sequence comprises a nucleic acid sequence of at least 1 Kb and having at least 90%, 95% or 99% sequence identity with a nongenic sequence selected from the group consisting of loci_137693_G1 (SEQ ID NO:387), loci_265551_G1 (SEQ ID NO:463), loci_128078_G1 (SEQ ID NO:560), loci_168286_G1 (SEQ ID NO:573), loci_3733_G1 (SEQ ID NO:1268), loci_203075_G1 (SEQ ID NO:2030), loci_232484_G1 (SEQ ID NO:2053), loci_136086_G1 (SEQ ID NO:4425), loci_203704_G1 (SEQ ID NO:2033), loci_127268_G1 (SEQ ID NO:2709), loci_204637_G1 (SEQ ID NO:2731), loci_291068_G1 (SEQ ID NO:3230), loci_232222_G1 (SEQ ID NO:3357), loci_43577_G1 (SEQ ID NO:3428), loci_204726_G1 (SEQ ID NO:424), loci_232228_G1 (SEQ ID NO: 4529) and a DNA of interest, wherein the DNA of interest is inserted into said nongenic sequence to produce said recombinant sequence. In accordance with embodiment 2 a recombinant sequence of embodiment 1 is provided wherein said DNA of interest is inserted proximal to a zinc finger target site specific to the nongenic sequence, and more particularly a zinc finger target site of Table 8. In accordance with embodiment 3 a recombinant sequence of embodiment 1 is provided, wherein said DNA of interest is inserted between a pair of zinc finger target sites specific to the nongenic sequence, and more particularly a pair of zinc finger target sites selected from Table 8. In accordance with one embodiment a recombinant sequence is provided wherein, said recombinant sequence consists of a nucleic acid sequence of at least 1 Kb and having 100% sequence identity with a sequence present in a nongenic sequence selected from the group consisting of loci_137693_G1 (SEQ ID NO:387), loci_265551_G1 (SEQ ID NO:463), loci_128078_G1 (SEQ ID NO:560), loci_168286_G1 (SEQ ID NO:573), loci_3733_G1 (SEQ ID NO:1268), loci_203075_G1 (SEQ ID NO:2030), loci_232484_G1 (SEQ ID NO:2053), loci_136086_G1 (SEQ ID NO:4425), loci_203704_G1 (SEQ ID NO:2033), loci_127268_G1 (SEQ ID NO:2709), loci_204637_G1 (SEQ ID NO:2731), loci_291068_G1 (SEQ ID NO:3230), loci_232222_G1 (SEQ ID NO:3357), loci_43577_G1 (SEQ ID NO:3428), loci_204726_G1 (SEQ ID NO:424), loci_232228_G1 (SEQ ID NO: 4529) and a DNA of interest, wherein the DNA of interest is inserted into said nongenic sequence to produce said recombinant sequence.

In accordance with embodiment 4 a recombinant sequence of any one of embodiments 1, 2 or 3 is provided wherein said DNA of interest comprises an analytical domain. In accordance with embodiment 5 a recombinant sequence of any one of embodiments 1, 2 or 3 is provided wherein said DNA of interest does not encode a peptide. In accordance with embodiment 6 a recombinant sequence of any one of embodiments 1, 2 or 3 is provided wherein said DNA of interest encodes a peptide. In accordance with embodiment 7 a recombinant sequence of embodiment 6 is provided wherein said DNA of interest comprises a gene expression cassette comprising an insecticidal resistance gene, herbicide tolerance gene, nitrogen use efficiency gene, water use efficiency gene, nutritional quality gene, DNA binding gene, and selectable marker gene. In accordance with embodiment 8 a recombinant sequence of any one of embodiments 1-7 is provided wherein said DNA of interest comprises two or more gene expression cassettes. In accordance with embodiment 9 a recombinant sequence of embodiment 8 is provided wherein two or more of said nongenic sequences each comprise an inserted DNA of interest to produce two or more recombinant sequences wherein the two or more recombinant sequences are located on a same chromosome. In accordance with embodiment 10 a recombinant sequence of any one of embodiments 1-9 is provided wherein said DNA of interest and/or said nongenic sequence are modified during insertion of said DNA of interest into said nongenic sequence. In accordance with embodiment 11 a maize plant, maize plant part, or maize plant cell is provided comprising a recombinant sequence of any one of embodiments 1-10. In accordance with embodiment 12 a method of making a transgenic plant cell comprising a DNA of interest is provided wherein the method comprises selecting a target nongenic maize genomic locus having at least 90%, 95% or 99% sequence identity from the group consisting of loci_137693_G1 (SEQ ID NO:387), loci_265551_G1 (SEQ ID NO:463), loci_128078_G1 (SEQ ID NO:560), loci_168286_G1 (SEQ ID NO:573), loci_3733_G1 (SEQ ID NO:1268), loci_203075_G1 (SEQ ID NO:2030), loci_232484_G1 (SEQ ID NO:2053), loci_136086_G1 (SEQ ID NO:4425), loci_203704_G1 (SEQ ID NO:2033), loci_127268_G1 (SEQ ID NO:2709), loci_204637_G1 (SEQ ID NO:2731), loci_291068_G1 (SEQ ID NO:3230), loci_232222_G1 (SEQ ID NO:3357), loci_43577_G1 (SEQ ID NO:3428), loci_204726_G1 (SEQ ID NO:424), loci_232228_G1 (SEQ ID NO: 4529), selecting a site specific nuclease that specifically binds and cleaves said target nongenic maize genomic locus, optionally one selected from Table 8, introducing said site specific nuclease into a maize plant cell, introducing the DNA of interest into the plant cell, inserting the DNA of interest into said target nongenic maize genomic loci, and selecting transgenic plant cells comprising the DNA of interest targeted to said nongenic locus. In accordance with embodiment 18 a method of making a transgenic plant cell of embodiment 12 wherein said site specific nuclease is selected from the group consisting of a zinc finger nuclease, a CRISPR nuclease, a TALEN, a homing endonuclease or a meganuclease. In accordance with embodiment 19 a method of making a transgenic plant cell of embodiment 12 or 18 wherein said DNA of interest is integrated within said nongenic locus via a homology directed repair integration method. In accordance with embodiment 20 a method of making a transgenic plant cell of embodiment 12 or 18 wherein said DNA of interest is integrated within said nongenic locus via a non-homologous end joining integration method. In accordance with embodiment 21 a method of making a transgenic plant cell of embodiment 12, 18, 19 or 20 wherein two or more of said DNA of interest are inserted into two or more of said target nongenic maize genomic loci, optionally wherein the two or more of said target nongenic maize genomic loci are located on a same chromosome.

In accordance with embodiment 1 a purified nongenic maize sequence of at least 1 Kb and having at least 90%, 95% or 99% sequence identity with a nongenic sequence selected from the group consisting of loci_137693_G1 (SEQ ID NO:387), loci_265551_G1 (SEQ ID NO:463), loci_128078_G1 (SEQ ID NO:560), loci_168286_G1 (SEQ ID NO:573), loci_3733_G1 (SEQ ID NO:1268), loci_203075_G1 (SEQ ID NO:2030), loci_232484_G1 (SEQ ID NO:2053), loci_136086_G1 (SEQ ID NO:4425), loci_203704_G1 (SEQ ID NO:2033), loci_127268_G1 (SEQ ID NO:2709), loci_204637_G1 (SEQ ID NO:2731), loci_291068_G1 (SEQ ID NO:3230), loci_232222_G1 (SEQ ID NO:3357), loci_43577_G1 (SEQ ID NO:3428), loci_204726_G1 (SEQ ID NO:424), loci_232228_G1 (SEQ ID NO: 4529) is provided. In accordance with one embodiment a purified nongenic maize sequence is provided wherein, said sequence consists of a nucleic acid sequence of at least 1 Kb and having 100% sequence identity with a sequence present in a nongenic sequence selected from the group consisting of loci_137693_G1 (SEQ ID NO:387), loci_265551_G1 (SEQ ID NO:463), loci_128078_G1 (SEQ ID NO:560), loci_168286_G1 (SEQ ID NO:573), loci_3733_G1 (SEQ ID NO:1268), loci_203075_G1 (SEQ ID NO:2030), loci_232484_G1 (SEQ ID NO:2053), loci_136086_G1 (SEQ ID NO:4425), loci_203704_G1 (SEQ ID NO:2033), loci_127268_G1 (SEQ ID NO:2709), loci_204637_G1 (SEQ ID NO:2731), loci_291068_G1 (SEQ ID NO:3230), loci_232222_G1 (SEQ ID NO:3357), loci_43577_G1 (SEQ ID NO:3428), loci_204726_G1 (SEQ ID NO:424), loci_232228_G1 (SEQ ID NO: 4529)

EXAMPLES Example 1: Identification of Targetable Genomic Loci in Zea mays

The Zea mays genome was screened with a bioinformatics approach using specific criteria to select optimal genomic loci for targeting of a polynucleotide donor. The specific criteria used for selecting the genomic loci were developed using considerations for optimal expression of a transgene within the plant genome, considerations for optimal binding of genomic DNA by a site specific DNA-binding protein, and transgenic plant product development requirements. In order to identify and select the genomic loci, genomic and epigenomic datasets of the Zea mays genome were scanned using a bioinformatics approach. Screening genomic and epigenomic datasets resulted in select loci which met the following criteria: 1) hypomethylated and greater than 1 Kb in length; 2) targetable via site specific nuclease-mediated integration of a polynucleotide donor; 3) agronomically neutral or non-genic; 4) regions from which an integrated transgene can be expressed; and 5) regions with recombination within/around the locus. Accordingly, a total of 5,286 genomic loci (SEQ ID NO:1-SEQ ID NO:5286) were identified using these specific criteria. The specific criteria are further described in detail below.

Hypomethylation

The Zea mays genome was scanned to select optimal genomic loci larger than 1 Kb that were DNA hypomethylated. Genome-wide DNA methylation levels of shoot and root tissue isolated from Zea mays c.v. B73 were surveyed via a bioinformatics method using Illumina™/Solexa™ 1G parallel sequencing data. The data were generated from genomic DNA isolated from the above described Zea mays plant tissues according to the protocol specified in Wang et al., (2009) Genome-Wide and Organ-Specific Landscapes of Epigenetic Modifications and Their Relationships to mRNA and Small RNA Transcriptomes in Maize. Plant Cell 21(4): 1053-1069). These data are available at the NCBI Genbank, Accession No; GEO:GSE15286. The raw sequencing reads were collected and mapped to the Zea mays c.v. B73 reference genome using the Bismark™ mapping software as described in Krueger F, Andrews S R (2011) Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27: 1571-1572).

The methylation level for each cytosine base in the genome was calculated as a percentage of the number of methylated reads mapping a particular cytosine base location to the total number of reads mapping to that location. The following hypothetical explains how methylation levels were calculated for each base within the Zea mays genome. For example, consider that there is a cytosine base at position 100 in chromosome 1 of the Zea mays c.v. B73 reference sequence. If there are a total of 20 reads mapped to cytosine base at position 100, and 10 of these reads are methylated, then the methylation level for the cytosine base at position 100 in chromosome 1 is estimated to be 50%. Accordingly, a profile of the methylation level for all of the genomic DNA base pairs obtained from the root and shoot tissue of Zea mays was calculated. The reads that could not be correctly mapped to unique locations in the Zea mays genome matched repetitive sequences that are widespread in the Zea mays genome, and are known in the art to be predominantly methylated.

Using the above described protocol, the methylation levels for the Zea mays c.v. B73 genome were measured. As such, regions of the Zea mays genome containing methylated reads indicated that these regions of the Zea mays genome were methylated. Conversely, the regions of the Zea mays genome that were absent of methylated reads indicated these regions of the Zea mays genome were non-methylated. The regions of the Zea mays genome from the shoot and root tissues that were non-methylated and did not contain any methylated reads are considered as “hypomethylated” regions. To make the root and shoot methylation profiles available for visualization, wiggle plots (http://useast.ensembl.org/info/website/upload/wig.html) were generated for each of the Zea mays c.v. B73 chromosomes. A screen-shot sample of a wiggle plot for the DNA methylation profile of root and shoot tissues obtained from Zea mays c.v. B73 chromosome number 1 is shown in FIG. 1.

The methylation profiles established for the Zea mays c.v. B73 root and shoot tissues, as described above, were combined into a consensus methylation profile and used to identify hypomethylated regions in the Zea mays c.v. B73 genome. The resulting Zea mays genomic consensus methylation profile was scanned to identify genomic locations without evidence of methylation, i.e. does not contain mapped methylated reads. Stretches of genomic DNA longer than 100 bp that were hypomethylated were identified. The specific length of each of these hypomethylated regions was calculated by determining the total number of base pairs between two genomic regions that showed evidence of methylation. Table 1 summarizes the identified hypomethylated regions. In addition, a distribution of the lengths of the hypomethylated regions of the Zea mays c.v. B73 genome is shown in FIG. 2.

TABLE 1 Hypomethylation profile of Zea mays c.v. B73 genome. Total Zea mays c.v. B73 genome size ~2.1 Gb Total combined length of hypomethylated region ~663 Mb (31.5% of the Zea mays c.v. B73 genome) Number of hypomethylated regions above 100 Bp 1,564,310 Number of hypomethylated regions above 1 Kb 130,917 Number of hypomethylated regions above 2 Kb 47,045 Number of hypomethylated regions above 10 Kb 206 Minimum length of hypomethylated region 100 Bp Maximum length of hypomethylated region 90,202 Bp

These hypomethylated regions of the Zea mays c.v. B73 genome were further characterized to identify and select specific genomic loci as the methylation free context of these regions indicated the presence of open chromatin. As such, all subsequent analyses were conducted on the identified hypomethylated regions.

Targetability

The hypomethylated sites identified in the Zea mays c.v. B73 were further analyzed to determine which sites were targetable via site specific nuclease-mediated integration of a polynucleotide donor. The Zea mays genome is known in the art to contain long stretches of highly repetitive DNA that are methylated and have high levels of sequence duplication. Annotation information of known repetitive regions in the Zea mays genome was collected from the Maize Genome Database (available at http://www.maizegdb.org/, and Lawrence, C J et al (2008) MaizeGDB: The Maize Model Organism Database for Basic, Translational, and Applied Research. Int J Plant Genomics. 2008:496957).

Accordingly, the hypomethylated sites identified above were screened to remove any sites that aligned with known repetitive regions annotated on the maize genome. The remaining hypomethylated sites that passed this first screen were subsequently scanned using a BLAST™ based homology search of a maize genomic database via the NCBI BLAST™ software (version 2.2.23) run using default parameter settings (Stephen F. Altschul et al (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402). As a result of the BLAST™ screen, any hypomethylated sites that had significant matches elsewhere in the genome, with sequence alignment coverage of over 40%, were removed from further analyses.

Agronomically Neutral or Nongenic

The hypomethylated sites identified in the Zea mays c.v. B73 were further analyzed to determine which sites were agronomically neutral or nongenic. As such, the hypomethylated sites described above were screened to remove any sites that overlapped or contained any known or predicted endogenous Zea mays c.v. B73 coding sequences. For this purpose, annotation data of known genes and mapping information of expressed sequence tag (EST) data were collected from Maize Genomic Database (available at www.maizegdb.org and Monaco, M., et al., Maize Metabolic Network Construction and Transcriptome Analysis.

doi:10.3835/plantgenome2012.09.0025; Posted online 23 Jan. 2013). Any genomic region immediately 2 Kb upstream and 1 Kb downstream to an open reading frame were also considered. These upstream and downstream regions may contain known or unknown conserved regulatory elements that are essential for gene function. The hypomethylated sites previously described above were analyzed for the presence of the known genes (including the 2 Kb upstream and 1 Kb downstream regions) and ESTs. Any hypomethylated sites that aligned with or overlapped with known genes (including the 2 Kb upstream and 1 Kb downstream regions) or ESTs were removed from downstream analysis. Expression

The hypomethylated sites identified in the Zea mays c.v. B73 were further analyzed to determine which sites were within proximity to an expressed maize gene. The transcript level expression of Zea mays genes was measured by analyzing transcriptome profiling data generated from Zea mays c.v. B73 root and shoot tissues using RNAseq™ technology as described in Wang et al., (2009) Genome-Wide and Organ-Specific Landscapes of Epigenetic Modifications and Their Relationships to mRNA and Small RNA Transcriptomes in Maize. Plant Cell. 21(4): 1053-1069. For each hypomethylated site, an analysis was completed to identify any annotated genes present within a 40 Kb region in proximity of the hypomethylated site, and an average expression level of the annotated gene(s) located in proximity to the hypomethylated site. Hypomethylated sites located greater than 40 Kb from an annotated gene with a non-zero average expression level were determined to not be proximal to an expressed Zea mays gene and were removed from further analyses.

Recombination

The hypomethylated sites identified in the Zea mays c.v. B73 were further analyzed to determine which sites had evidence of recombination and could facilitate introgression of the optimal genomic loci into other lines of Zea mays via conventional breeding. Diverse Zea mays genotypes are routinely crossed during conventional breeding to develop new and improved Zea mays lines containing traits of agronomic interest. As such, agronomic traits that are introgressed into optimal genomic loci within a Zea mays line via plant-mediated transformation of a transgene should be capable of further being introgressed into other Zea mays lines, especially elite lines, via meiotic recombination during conventional plant breeding. The hypomethylated sites described above were screened to identify and select sites that possessed some level of meiotic recombination. Any hypomethylated sites that were present within chromosomal regions characterized as recombination “cold-spots” were identified and removed. In Zea mays, these cold spots were defined using a high resolution marker dataset generated from multiple mapping populations. (Jafar Mammadov, Wei Chen, Anastasia Chueva, Karthik Muthuraman, Ruihua Ren, David Meyer, and Siva Kumpatla. 2011. Distribution of Recombinant Frequencies across the Maize Genome. 52^(nd) Annual Maize Genetics Conference).

The meiotic recombination frequencies between any pair of Zea mays genomic markers across a chromosome were calculated based on the ratio of the genetic distance between markers (in centimorgan (cM)) to the physical distance between the markers (in megabases (Mb)). For example, if the genetic distance between a pair of markers was 1 cM, and the physical distance between the same pair of markers was 2 Mb, then the calculated recombination frequency was determined to be 0.5 cM/Mb. For each hypomethylated site identified above, a pair of markers at least 1 Mb apart was chosen and the recombination frequency was calculated. Deployment of this method was used to calculate the recombination frequency of the hypomethylated sites. Any hypomethylated sites with a recombination frequency of 0.00041 cM/Mb were identified and removed from further analysis. The remaining hypomethylated regions comprising a recombination frequency greater than 0.00041 cM/Mb were selected for further analysis.

Identification of Optimal Genomic Loci

Application of the selection criteria described above resulted in the identification of a total of 52,885 optimal genomic loci from the Zea mays genome. Table 2 summarizes the lengths of the identified optimal genomic loci. These optimal genomic loci possess the following characteristics: 1) hypomethylated genomic loci greater than 1 Kb in length; 2) genomic loci that are targetable via site specific nuclease-mediated integration of a polynucleotide donor; 3) genomic loci that are agronomically neutral or nongenic; 4) genomic loci from which a transgene can be expressed; and 5) evidence of recombination within the genomic loci. Of all of the optimal genomic loci described in Table 2, only the optimal genomic loci that were greater than 1 Kb were further analyzed and utilized for targeting of a donor polynucleotide sequence. The sequences of these optimal genomic loci are disclosed as SEQ ID NO:1-SEQ ID NO:5,286. Collectively, these optimal genomic loci are locations within the Zea mays genome that can be targeted with a donor polynucleotide sequence, as further demonstrated herein below.

TABLE 2 Lists the size range of optimal genomic loci identified in the Zea mays genome that are hypomethylated, show evidence of recombination, targetable, agronomically neutral or nongenic, and are in proximity to an expressed endogenous gene. Number of optimal genomic loci larger than 100 Bp 52,885 Number of optimal genomic loci larger than 1 Kb 5,286 Number of optimal genomic loci larger than 2 Kb 770 Number of optimal genomic loci larger than 4 Kb 16

Example 2: F-Distribution and Principal Component Analysis to Cluster Optimal Genomic Loci from Zea mays

The 5,286 identified optimal genomic loci (SEQ ID NO: 1-SEQ ID NO: 5,286) were further analyzed using the F-distribution and Principal Component Analysis statistical methods to define a representative population and clusters for grouping of the optimal genomic loci.

F-Distribution Analysis

The identified 5,286 optimal genomic loci were statistically analyzed using a continuous probability distribution statistical analysis. As an embodiment of the continuous probability distribution statistical analysis, an F-distribution test was completed to determine a representative number of optimal genomic loci. The F-distribution test analysis was completed using equations and methods known by those with skill in the art. For more guidance, the F-distribution test analysis as described in K. M Remund, D. Dixon, D L. Wright and L R. Holden. Statistical considerations in seed purity testing for transgenic traits. Seed Science Research (2001) 11, 101-119, herein incorporated by reference, is a non-limiting example of an F-distribution test. The F-distribution test assumes random sampling of the optimal genomic loci, so that any non-valid loci are evenly distributed across the 5,286 optimal genomic loci, and that the number of optimal genomic loci sampled is 10% or less of the total population of 5,286 optimal genomic loci.

The F-distribution analysis indicated that 72 of the 5,286 optimal genomic loci provided a representative number of the 5,286 optimal genomic loci, at a 95% confidence level. Accordingly, the F-distribution analysis showed that if 72 optimal genomic loci were tested and all were targetable with a donor polynucleotide sequence, then these results would indicate that 96% or more of the 5,286 optimal genomic loci are positive at the 95% confidence level. The best estimate of validating the total percentage of the 5,286 optimal genomic loci would be if 100% of the 72 tested optimal genomic loci were targetable. Accordingly, 96% is actually the lower bound of the true percent validated at the 95% confidence level. This lower bound is based on the 0.95 quantile of the F-distribution, for the 95% confidence level. (Remund K, Dixon D, Wright D, and Holden L. Statistical considerations in seed purity testing for transgenic traits. Seed Science Research (2001) 11, 101-119).

Principal Component Analysis

Next, a Principal Component Analysis (PCA) statistical method was completed to further assess and visualize similarities and differences of the data set comprising the 5,286 identified optimal genomic loci to enable sampling of diverse loci for targeting validation. The PCA involves a mathematical algorithm that transforms a larger number of correlated variables into a smaller number of uncorrelated variables called principal components.

The PCA was completed on the 5,286 identified optimal genomic loci by generating a set of calculable features or attributes that could be used to describe the 5,286 identified optimal genomic loci. Each feature is numerically calculable and is defined specifically to capture the genomic and epigenomic context of the 5,286 identified optimal genomic loci. A set of 10 features for each Zea mays optimal genomic loci was identified and are described in greater detail below.

1. Length of the optimal genomic loci

-   -   a. The length of the optimal genomic loci in this data set         ranged from a minimum of 1,000 Bp to a maximum of 8,267 Bp.

2. Recombination frequency in a 1 MB region around the optimal genomic loci

-   -   a. In maize, recombination frequency for a chromosomal location         was defined using an internal high resolution marker dataset         generated from multiple mapping populations (Jafar Mammadov, Wei         Chen, Anastasia Chueva, Karthik Muthuraman, Ruihua Ren, David         Meyer, and Siva Kumpatla. 2011. Distribution of Recombinant         Frequencies across the Maize Genome. 52^(nd) Annual Maize         Genetics Conference).     -   b. Recombination frequencies between any pairs of markers across         the chromosome were calculated based on the ratio of the genetic         distance between markers (in centimorgan (cM)) to the physical         distance between the markers (in Mb). For example, if the         genetic distance between a pair of markers is 1 cM and the         physical distance between the same pairs of markers is 2 Mb, the         calculated recombination frequency is 0.5 cM/Mb. For each         optimal genomic loci, a pair of markers at least 1 Mb apart was         chosen and the recombination frequency was calculated in this         manner. These recombination values ranged from a minimum of         0.00041 cM/Mb to a maximum of 62.42 cM/Mb.

3. Level of optimal genomic loci sequence uniqueness

-   -   a. For each optimal genomic loci, the nucleotide sequence of the         optimal genomic loci was scanned against the Zea mays c.v. B73         genome using a BLAST™ based homology search using the NCBI         BLAST™ software (version 2.2.23) run using the default parameter         settings (Stephen F. Altschul et al (1997), “Gapped BLAST and         PSI-BLAST: a new generation of protein database search         programs”, Nucleic Acids Res. 25:3389-3402). As these optimal         genomic loci sequences are identified from the Zea mays c.v. B73         genome, the first BLAST™ hit identified through this search         represents the Zea mays c.v. B73 sequence itself. The second         BLAST™ hit for each optimal genomic loci sequence was identified         and the alignment coverage (represented as the percent of the         optimal genomic loci covered by the BLAST™ hit) of the hit was         used as a measure of uniqueness of the optimal genomic loci         sequence within the Zea mays genome. These alignment coverage         values for the second BLAST™ hit ranged from a minimum of 0% to         a maximum of 39.98% sequence identity. Any sequences that         aligned at higher levels of sequence identity were not         considered.

4. Distance from the optimal genomic loci to the closest gene in its neighborhood

-   -   a. Gene annotation information and the location of known genes         in the Zea mays genome were extracted from Maize Genome Database         (available at, www.maizegdb.org and Monaco, M., et al., Maize         Metabolic Network Construction and Transcriptome Analysis.         doi:10.3835/plantgenome2012.09.0025; Posted online 23 Jan.         2013). For each optimal genomic loci, the closest annotated         gene, considering both upstream and downstream locations, was         identified and the distance between the optimal genomic loci         sequence and the gene was measured (in Bp). For example, if a         optimal genomic locus is located in chromosome 1 from position         500 to position 1500, and the closest gene to this optimal         genomic locus is located in chromosome 1 from position 2000 to         position 3000, the distance from the optimal genomic loci to         this closest gene is calculated to be 500 Bp. These values for         all 5,286 of the optimal genomic loci dataset ranged from a         minimum of 1001 Bp to a maximum of 34,809 Bp.

5. GC % in the optimal genomic loci sequence

-   -   a. For each optimal genomic locus, the nucleotide sequence was         analyzed to estimate the number of Guanine and Cytosine bases         present. This count was represented as a percentage of the         sequence length of each optimal genomic locus and provides a         measure for GC %. These GC % values for the maize optimal         genomic loci dataset range from 25.17% to 68.3%.

6. Number of genes in a 40 Kb neighborhood around the optimal genomic loci sequence

-   -   a. Gene annotation information and the location of known genes         in the Zea mays c.v. B73 genome were extracted from Maize Genome         Database. For each of the 5,286 optimal genomic loci sequence, a         40 Kb window around the optimal genomic loci sequence was         defined and the number of annotated genes with locations         overlapping this window was counted. These values ranged from a         minimum of 1 gene to a maximum of 9 genes within the 40 Kb         neighborhood.

7. Average gene expression in a 40 Kb neighborhood around the optimal genomic loci

-   -   a. Transcript level expression of maize genes was measured by         analyzing available transcriptome profiling data generated from         Zea mays c.v. B73 root and shoot tissues using RNAseq™         technology (Mortazavi, A. et al., Mapping and quantifying         mammalian transcriptomes by RNA-Seq. Nat. Methods. 5, 621-628         (2008); Wang et al., Genome-Wide and Organ-Specific Landscapes         of Epigenetic Modifications and Their Relationships to mRNA and         Small RNA Transcriptomes in Maize. Plant Cell. 2009 April;         21(4): 1053-1069). Gene annotation information and the location         of known genes in the Zea mays c.v. B73 genome were extracted         from Maize Genome Database For each optimal genomic locus,         annotated genes within the Zea mays c.v. B73 genome that were         present in a 40 Kb neighborhood around the optimal genomic loci         were identified. Expression levels for each of the genes were         extracted from the transcriptome profiles described in the above         referenced citations and an average gene expression level was         calculated. Expression values of all genes within the genome of         Zea mays vary greatly. The minimum expression value is 0 and the         maximum expression value is 2511.397, with a mean expression         value of 18.489 and a median expression value of 3.604. The         average expression values for all of the 5,286 optimal genomic         loci dataset ranged from a minimum of 0.00369 to a maximum of         2233.06.

8. Level of nucleosome occupancy around the optimal genomic loci

-   -   a. Understanding the level of nucleosome occupancy for a         particular nucleotide sequence provides information about         chromosomal functions and the genomic context of the sequence.         The NuPoP™ statistical package was used to predict the         nucleosome occupancy and the most probable nucleosome         positioning map for any size of genomic sequences (Xi, L.,         Fondufe-Mittendor, Y., Xia, L., Flatow, J., Widom, J. and Wang,         J.-P., Predicting nucleosome positioning using a duration Hidden         Markov Model, BMC Bioinformatics, 2010,         doi:10.1186/1471-2105-11-346.). For each of the 5,286 optimal         genomic loci, the nucleotide sequence was submitted for analysis         with the NuPoP™ software and a nucleosome occupancy score was         calculated. These nucleosome occupancy scores for the maize         optimal genomic loci dataset ranged from a minimum of 0 to a         maximum of 0.962.

9. Relative location within the chromosome (proximity to centromere)

-   -   a. A centromere is a region on a chromosome that joins two         sister chromatids. The portions of a chromosome on either side         of the centromere are known as chromosomal arms. Genomic         locations of centromeres on all 10 Maize chromosomes were         identified in the published Zea mays c.v. B73 reference sequence         (Schnable, P., et al., (2009) The B73 maize genome: complexity,         diversity and dynamics. Science, 326(5956): 1112-1115).         Information on the position of the centromere in each of the Zea         mays chromosomes and the lengths of the chromosome arms was         extracted from Maize Genome Database. For each optimal genomic         locus, the genomic distance from the optimal genomic locus         sequence to the centromere of the chromosome that it is located         on, is measured (in Bp). The relative location of optimal         genomic loci within the chromosome is represented as the ratio         of its genomic distance to the centromere relative to the length         of the specific chromosomal arm that it lies on. These relative         location values for the maize optimal genomic loci dataset         ranged from a minimum of 0.00373 to a maximum of 0.99908 ratio         of genomic distance.

10. Number of optimal genomic loci in a 1 Mb region

-   -   a. For each optimal genomic loci, a 1 Mb genomic window around         the optimal genomic loci location was defined and the number of         other, additional optimal genomic loci present within or         overlapping this region were calculated, including the optimal         genomic loci under consideration. The number of optimal genomic         loci in a 1 Mb ranged from a minimum of 1 to a maximum of 22.

All of the 5,286 optimal genomic loci were analyzed using the features and attributes described above. The results or values for the score of the features and attributes of each optimal genomic locus are further described in Table 3 (herein incorporated by reference as a separate electronic filing). The resulting dataset was used in the PCA statistical method to cluster the 5,286 identified optimal genomic loci into clusters. During the clustering process, after estimating the “p” principle components of the optimal genomic loci, the assignment of the optimal genomic loci to one of the 32 clusters proceeded in the “p” dimensional Euclidean space. Each of the “p” axes was divided into “k” intervals. Optimal genomic loci assigned to the same interval were grouped together to form clusters. Using this analysis, each PCA axis was divided into two intervals, which was chosen based on a priori information regarding the number of clusters required for experimental validation. All analysis and the visualization of the resulting clusters were carried out with the Molecular Operating Environment™ (MOE) software from Chemical Computing Group Inc. (Montreal, Quebec, Canada).

The PCA approach was used to cluster the set of 5,286 identified optimal genomic loci into 32 distinct clusters based on their feature values, described above. During the PCA process, five principal components (PC) were generated, with the top three PCs containing about 90% of the total variation in the dataset (Table 4). These three PCAs were used to graphically represent the 32 clusters in a three dimensional plot (FIG. 3). After the clustering process, was completed, one representative optimal genomic locus was chosen from each cluster. This was performed by choosing a select optimal genomic locus, within each cluster, that was closest to the centroid of that cluster (Table 4). The chromosomal locations of the 32 representative optimal genomic loci are uniformly distributed among the 10 maize chromosomes and are not biased toward any particular genomic location, as shown in FIG. 4.

TABLE 4 Description of the 32 maize representative optimal genomic loci identified from the PCA Optimal Genomic Loci Length Cluster SEQ ID Name Genomic Location (Bp) Number NO: optimal_loci_59517_G1 chr2: 43352132 . . . 43353146 1015 1 1 optimal_loci_159525_G1 chr4: 172518643 . . . 172519712 1070 2 199 optimal_loci_9811_G1 chr1: 52159463 . . . 52161841 2379 3 365 optimal_loci_7507_G1 chr1: 39334848 . . . 39337271 2424 4 543 optimal_loci_178978_G1 chr5: 35776311 . . . 35777560 1250 5 687 optimal_loci_285621_G1 chr8: 118321357 . . . 118322528 1172 6 875 optimal_loci_221721_G1 chr6: 91309097 . . . 91311722 2626 7 1089 optimal_loci_83937_G1 chr2: 192746622 . . . 192748862 2241 8 1233 optimal_loci_37146_G1 chr1: 223833176 . . . 223834563 1388 9 1369 optimal_loci_156393_G1 chr4: 154313884 . . . 154315253 1370 10 1571 optimal_loci_343678_G1 chr10: 113837795 . . . 113839503 1709 11 1795 optimal_loci_60209_G1 chr2: 47513705 . . . 47515145 1441 12 1980 optimal_loci_282323_G1 chr8: 100763204 . . . 100764398 1195 13 2171 optimal_loci_64542_G1 chr2: 72203716 . . . 72205045 1330 14 2349 optimal_loci_162531_G1 chr4: 189896984 . . . 189899332 2349 15 2557 optimal_loci_337001_G1 chr10: 77188319 . . . 77190007 1689 16 2693 optimal_loci_66202_G1 chr2: 83483805 . . . 83484909 1105 17 2855 optimal_loci_185454_G1 chr5: 80270170 . . . 80271254 1085 18 3004 optimal_loci_239863_G1 chr7: 14997553 . . . 14999296 1744 19 3151 optimal_loci_257541_G1 chr7: 125978470 . . . 125980969 2500 20 3289 optimal_loci_217939_G1 chr6: 67227678 . . . 67228708 1031 21 3455 optimal_loci_326869_G1 chr10: 12348441 . . . 12349499 1059 22 3586 optimal_loci_31710_G1 chr1: 194939396 . . . 194943360 3965 23 3731 optimal_loci_81941_G1 chr2: 181418576 . . . 181421181 2606 24 3849 optimal_loci_198387_G1 chr5: 164712378 . . . 164713567 1190 25 3981 optimal_loci_197372_G1 chr5: 158680601 . . . 158681681 1081 26 4192 optimal_loci_106202_G1 chr3: 85647138 . . . 85648635 1498 27 4401 optimal_loci_232228_G1 chr6: 144719567 . . . 144723469 3903 28 4529 optimal_loci_244324_G1 chr7: 40299412 . . . 40300584 1173 29 4646 optimal_loci_157315_G1 chr4: 158710709 . . . 158711983 1275 30 4836 optimal_loci_137489_G1 chr4: 29898267 . . . 29899725 1459 31 5046 optimal_loci_31764_G1 chr1: 195178584 . . . 195182163 3580 32 5162 Final Selection of 72 Genomic Loci for Targeting of a Polynucleotide Donor Polynucleotide Sequence

A total of 72 genomic loci were identified and selected for targeting with a donor polynucleotide sequence from the 5,286 genomic loci that were clustered within 32 distinct clusters. For each of the 32 clusters, a representative genomic locus (32 representative genomic loci that were closest to the centroid of that cluster as described above in Table 4) and an additional genomic locus within each cluster were chosen. The additional optimal genomic loci were selected by first screening all of the 5,286 selected optimal genomic sequences against a whole genome database consisting of genomic DNA sequence data for both Zea mays c.v. Hi-II (targeting screening line) and Zea mays c.v. B104 (transformation line) to determine the coverage (how many optimal genomic loci were present in both genomes) and percentage of sequence identity in the genome from both lines. The additional optimal genomic loci with 100% coverage (the entire sequence length of the optimal loci aligned between both genomes) and 100% identity in both the Hi-II and B104 genomic databases were selected for targeting validation (FIG. 5). Comparatively, a small number of the representative genomic loci had sequence identity that was less than 100% coverage and identity in both the Hi-II and B104 genomic database (FIG. 5). Other criteria such as genomic loci size, extent of uniqueness, GC % content and chromosomal distribution of the optimal genomic loci were also taken into consideration in selecting the additional optimal genomic loci. The chromosomal location of the 72 selected optimal genomic loci and the specific genomic configuration of each Zea mays optimal genomic loci are shown in FIG. 6 and Table 5, respectively.

TABLE 5 Description of the maize selected optimal genomic loci chosen for targeting validation. From these optimal genomic loci listed in this table, 72 maize optimal genomic loci are representative of the identified total of 5,286 maize selected optimal genomic loci. SEQ Optimal Genomic Loci Length Cluster ID Name Genomic Location (bp) Number NO: optimal_loci_59517_G1 chr2: 43352132 . . . 43353146 1015 1 1 optimal_loci_25001_G1 chr1: 151371224 . . . 151372260 1037 1 100 optimal_loci_112632_G1 chr3: 128098856 . . . 128100257 1402 2 203 optimal_loci_28905_G1 chr1: 177037718 . . . 177038919 1202 2 295 optimal_loci_129164_G1 chr3: 221246027 . . . 221247542 1516 3 384 optimal_loci_204726_G1 chr5: 200665730 . . . 200670667 4938 3 424 optimal_loci_2425_G1 chr1: 12810845 . . . 12814490 3646 3 451 optimal_loci_122036_G1 chr3: 184608166 . . . 184609697 1532 4 547 optimal_loci_5735_G1 chr1: 29190279 . . . 29192844 2566 4 671 optimal_loci_178978_G1 chr5: 35776311 . . . 35777560 1250 5 687 optimal_loci_288388_G1 chr8: 133290442 . . . 133291481 1040 5 781 optimal_loci_60310_G1 chr2: 47967092 . . . 47968271 1180 5 843 optimal_loci_285621_G1 chr8: 118321357 . . . 118322528 1172 6 875 optimal_loci_243330_G1 chr7: 34630402 . . . 34631577 1176 6 967 optimal_loci_127038_G1 chr3: 210603611 . . . 210605198 1588 7 1107 optimal_loci_262784_G1 chr7: 155767046 . . . 155769049 2004 7 1147 optimal_loci_344662_G1 chr10: 119131667 . . . 119133955 2289 7 1190 optimal_loci_153894_G1 chr4: 139979597 . . . 139981225 1629 8 1252 optimal_loci_28771_G1 chr1: 176062139 . . . 176063611 1473 8 1300 optimal_loci_1098_G1 chr1: 5582601 . . . 5583834 1234 9 1371 optimal_loci_97772_G1 chr3: 30209253 . . . 30210607 1355 9 1569 optimal_loci_156393_G1 chr4: 154313884 . . . 154315253 1370 10 1571 optimal_loci_236662_G1 chr6: 165975716 . . . 165977010 1295 10 1663 optimal_loci_139485_G1 chr4: 42804231 . . . 42805751 1521 11 1822 optimal_loci_301175_G1 chr9: 20325171 . . . 20326621 1451 11 1906 optimal_loci_152337_G1 chr4: 130033092 . . . 130035481 2390 12 2003 optimal_loci_202616_G1 chr5: 188822901 . . . 188824814 1914 12 2027 optimal_loci_203704_G1 chr5: 194836270 . . . 194840217 3948 12 2033 optimal_loci_282323_G1 chr8: 100763204 . . . 100764398 1195 13 2171 optimal_loci_262782_G1 chr7: 155759080 . . . 155760097 1018 13 2256 optimal_loci_64542_G1 chr2: 72203716 . . . 72205045 1330 14 2349 optimal_loci_236455_G1 chr6: 164795991 . . . 164797027 1037 14 2428 optimal_loci_162531_G1 chr4: 189896984 . . . 189899332 2349 15 2557 optimal_loci_301774_G1 chr9: 23468085 . . . 23470278 2194 15 2632 optimal_loci_344663_G1 chr10: 119143167 . . . 119144795 1629 15 2649 optimal_loci_337001_G1 chr10: 77188319 . . . 77190007 1689 16 2693 optimal_loci_204637_G1 chr5: 200298202 . . . 200301414 3213 16 2731 optimal_loci_238100_G1 chr7: 4899227 . . . 4900708 1482 16 2753 optimal_loci_66202_G1 chr2: 83483805 . . . 83484909 1105 17 2855 optimal_loci_264359_G1 chr7: 163504241 . . . 163505487 1247 17 2934 optimal_loci_282653_G1 chr8: 102704765 . . . 102705924 1160 18 3086 optimal_loci_80282_G1 chr2: 173420834 . . . 173421870 1037 18 3139 optimal_loci_291068_G1 chr8: 148277606 . . . 148279985 2380 19 3230 optimal_loci_56395_G1 chr2: 24801482 . . . 24803132 1651 19 3270 optimal_loci_200497_G1 chr5: 176879526 . . . 176881345 1820 20 3334 optimal_loci_232222_G1 chr6: 144700575 . . . 144702126 1552 20 3357 optimal_loci_43577_G1 chr1: 256469704 . . . 256472666 2963 20 3428 optimal_loci_5607_G1 chr1: 28613065 . . . 28615113 2049 20 3435 optimal_loci_114664_G1 chr3: 140106950 . . . 140108061 1112 21 3457 optimal_loci_228254_G1 chr6: 126085629 . . . 126086823 1195 21 3497 optimal_loci_120993_G1 chr3: 179419306 . . . 179420357 1052 22 3593 optimal_loci_53137_G1 chr2: 7304197 . . . 7305496 1300 22 3702 optimal_loci_31710_G1 chr1: 194939396 . . . 194943360 3965 23 3731 optimal_loci_344664_G1 chr10: 119144946 . . . 119146850 1905 23 3815 optimal_loci_81941_G1 chr2: 181418576 . . . 181421181 2606 24 3849 optimal_loci_321514_G1 chr9: 140776147 . . . 140777584 1438 24 3939 optimal_loci_198387_G1 chr5: 164712378 . . . 164713567 1190 25 3981 optimal_loci_301180_G1 chr9: 20328932 . . . 20330129 1198 25 4113 optimal_loci_197372_G1 chr5: 158680601 . . . 158681681 1081 26 4192 optimal_loci_348776_G1 chr10: 142097590 . . . 142098803 1214 26 4350 optimal_loci_244439_G1 chr7: 41068791 . . . 41070248 1458 27 4458 optimal_loci_348258_G1 chr10: 139297032 . . . 139298517 1486 27 4487 optimal_loci_232228_G1 chr6: 144719567 . . . 144723469 3903 28 4529 optimal_loci_322501_G1 chr9: 146078534 . . . 146080201 1668 28 4610 optimal_loci_244324_G1 chr7: 40299412 . . . 40300584 1173 29 4646 optimal_loci_97232_G1 chr3: 27463016 . . . 27464143 1128 29 4832 optimal_loci_157315_G1 chr4: 158710709 . . . 158711983 1275 30 4836 optimal_loci_282499_G1 chr8: 101771408 . . . 101772767 1360 30 4953 optimal_loci_155031_G1 chr4: 146991391 . . . 146993137 1747 31 5060 optimal_loci_301773_G1 chr9: 23465509 . . . 23467762 2254 31 5110 optimal_loci_283161_G1 chr8: 105321958 . . . 105323571 1614 32 5213 optimal_loci_55524_G1 chr2: 20099003 . . . 20100485 1483 32 5264 optimal_loci_127268_G1 chr3: 211767898 . . . 211770046 2149 16 2709 optimal_loci_136086_G1 chr4: 22531506 . . . 22534989 3484 27 4425 optimal_loci_232484_G1 chr6: 146122164 . . . 146125580 3417 12 2053 optimal_loci_203075_G1 chr5: 191370802 . . . 191374627 3826 12 2030 optimal_loci_3733_G1 chr1: 19232372 . . . 19235997 3626 11 1923 optimal_loci_168286_G1 chr4: 219987223 . . . 219990695 3473 4 573 optimal_loci_128078_G1 chr3: 215482594 . . . 215485640 3047 4 560 optimal_loci_265551_G1 chr7: 170127188 . . . 170130734 3547 3 463 optimal_loci_137693_G1 chr4: 31118968 . . . 31122359 3392 3 387

A large suite of 5,286 genomic locations have been identified in the Zea mays genome as optimal genomic loci for targeting with a donor polynucleotide sequence using precision genome engineering technologies. A statistical analysis approach was deployed to group the 5,286 selected genomic loci into 32 clusters with similar genomic contexts, and to identify a subset of 72 selected genomic loci representative of the set of 5,286 selected genomic loci. The 72 representative loci were validated as optimal genomic loci via targeting with a donor polynucleotide sequence. By performing the PCA statistical analysis for the numerical values generated for the ten sets of features or attributes that are described above, the ten features or attributes were computed into PCA components of fewer dimensions. As such, PCA components were reduced into five dimensions that are representative of the ten features or attributes described above (Table 6). Each PCA component is equivalent to a combination of the ten features or attributes described above. From these PCA components comprising five dimensions, as computed using the PCA statistical analysis, the 32 clusters were determined.

TABLE 6 The five PCA components (PCA1, PCA2, PCA3, PCA4, and PCA5) that define each of the 32 clusters and the sequences (SEQ ID NO: 1-SEQ ID NO: 5286) which make up each cluster. These five dimensions are representative of the ten features or attributes described above that were used to identify the optimal genomic loci. The minimum (Min), mean, median and maximum (Max) values for each PCA component are provided. Cluster4 Cluster9 Cluster10 Cluster11 Cluster12 Cluster13 Cluster1 Cluster2 Cluster3 (SEQ ID Cluster5 Cluster6 Cluster7 Cluster8 (SEQ (SEQ (SEQ (SEQ (SEQ (SEQ ID (SEQ ID (SEQ ID NO: (SEQ ID (SEQ ID (SEQ ID NO: (SEQ ID NO: ID NO: ID NO: ID NO: ID NO: ID NO: NO: 1--SEQ NO: 199--SEQ NO: 365--SEQ 543--SEQ NO: 687--SEQ NO: 875--SEQ 1089--SEQ 1233--SEQ 1369--SEQ 1571--SEQ 1795--SEQ 1980--SEQ 2171--SEQ ID ID ID ID ID ID ID ID ID ID ID ID ID NO: 198) NO: 364) NO: 542) NO: 686) NO: 874) NO: 1088) NO: 1232) NO: 1368) NO: 1570) NO: 1794) NO: 1979) NO: 2170) NO: 2348) PCA1 Min −0.38899 −0.93177 −0.39537 −0.93241 −0.39582 −0.93174 −0.38719 −0.93217 −0.38101 −0.93175 −0.39194 −0.93253 −0.38415 Mean 0.73994 −0.70291 0.797903 −0.72366 0.696097 −0.70419 0.759996 −0.69832 0.799943 −0.71434 0.770295 −0.73093 0.655148 Median 0.444732 −0.72051 0.581978 −0.72065 0.41229 −0.72032 0.468691 −0.71729 0.546926 −0.72051 0.347427 −0.72075 0.31035 Max 3.016652 −0.40085 3.06313 −0.40153 3.823763 −0.40276 3.007282 −0.40162 4.260435 −0.41456 3.072388 −0.402 3.054517 PCA2 Min 0.200459 0.211002 −9.82023 −5.15632 0.200591 0.233367 −4.04364 −4.90205 0.204949 0.205064 −5.36888 −6.75555 0.206839 Mean 0.607958 0.651683 −0.77754 −0.94886 0.62733 0.640492 −0.7257 −0.69802 0.613344 0.639532 −1.0031 −1.01406 0.618082 Median 0.616048 0.69582 −0.4007 −0.60703 0.654722 0.662685 −0.5115 −0.48357 0.642703 0.673247 −0.52447 −0.66079 0.639485 Max 0.941211 0.950602 0.188311 0.193638 0.933845 0.95102 0.194718 0.193615 0.950028 0.956661 0.197865 0.193687 0.950172 PCA3 Min −0.19912 −0.19998 −0.19915 −0.19817 −0.3145 −0.32531 −0.30392 −0.31372 −0.19958 −0.19843 −0.19868 −0.19755 −0.31583 Mean 0.251544 0.348751 0.153077 0.230562 −0.26578 −0.28236 −0.25128 −0.26153 0.244656 0.257424 0.121116 0.22983 −0.2653 Median −0.02809 −0.04129 −0.02763 −0.01853 −0.26978 −0.28873 −0.2537 −0.26577 −0.02402 −0.02638 −0.05745 −0.02841 −0.26895 Max 6.481119 34.90501 11.24551 10.67521 −0.20057 −0.20094 −0.20105 −0.20248 5.739189 11.2077 3.384549 16.92247 −0.20086 PCA4 Min −0.39542 −0.39731 −0.39369 −0.39886 −0.37619 −0.37126 −0.39716 −0.39684 −1.25027 −1.22084 −1.21449 −1.13853 −1.24332 Mean 1.030652 0.94334 0.839835 0.728573 1.088658 1.125488 0.837988 0.867379 −0.881 −0.83045 −0.8525 −0.80304 −0.87789 Median 0.956571 0.843296 0.664549 0.334136 1.025711 1.062969 0.491677 0.598316 −0.87578 −0.82491 −0.84403 −0.81514 −0.89279 Max 2.82969 2.82634 2.890302 2.848484 2.875967 2.891137 2.869785 2.792003 −0.41074 −0.40079 −0.43247 −0.41111 −0.4172 PCA5 Min −0.19722 −0.19899 −0.18939 −0.1958 −0.1959 −0.1976 −0.19078 −0.19095 −0.19058 −0.18616 −0.19615 −0.18815 −0.196 Mean 0.692886 0.757261 0.642033 0.698495 0.682658 0.693974 0.661659 0.618725 0.84803 0.77689 0.822063 0.791532 0.824284 Median 0.537914 0.609134 0.438724 0.587864 0.500322 0.514611 0.457563 0.432322 0.775864 0.59967 0.802156 0.730284 0.795933 Max 2.938322 4.205435 2.765824 2.808973 4.140417 2.995524 3.446519 2.717293 2.760305 2.593518 2.351784 2.947057 2.67123 Cluster14 (SEQ ID Cluster15 Cluster17 (SEQ Cluster18 (SEQ Cluster19 Cluster20 (SEQ Cluster21 (SEQ NO: 2349--SEQ (SEQ ID NO: Cluster16 (SEQ ID NO: 2854--SEQ ID NO: 3004--SEQ (SEQ ID NO: ID NO: 3289--SEQ ID NO: 3456--SEQ Cluster22 ID 2557--SEQ ID ID NO: 2693--SEQ ID ID 3151--SEQ ID ID ID (SEQ ID NO: 3586--SEQ NO: 2556) NO: 2692) ID NO: 2854) NO: 3003) NO: 3150) NO: 3288) NO: 3455) NO: 3585) ID NO: 3730) PCA1 Min −1.03449 −0.3984 −0.93226 −0.4 −0.93176 −0.3845 −0.93215 −0.39456 −0.93174 Mean −0.70636 0.519692 −0.72131 0.788093 −0.72141 0.822434 −0.7062 0.648476 −0.71986 Median −0.72054 0.149839 −0.72068 0.474147 −0.72052 0.469551 −0.72007 0.373243 −0.72054 Max −0.40125 2.973061 −0.4106 3.076914 −0.4042 3.022389 −0.40471 2.902287 −0.41693 PCA2 Min 0.206354 −4.6237 −4.17636 0.201471 0.200304 −12.4583 −5.15079 0.202767 0.202637 Mean 0.613673 −0.71726 −0.89472 0.585603 0.656596 −0.99953 −0.84736 0.618663 0.60694 Median 0.642803 −0.38947 −0.58265 0.600619 0.671923 −0.69949 −0.41126 0.650056 0.588239 Max 0.955582 0.178297 0.199158 0.947875 0.957912 0.189554 0.199151 0.949085 0.95292 PCA3 Min −0.3256 −0.30535 −0.31509 −0.19941 −0.19977 −0.19819 −0.19983 −0.31601 −0.32437 Mean −0.27114 −0.2528 −0.26165 0.635893 0.335092 0.188191 0.219518 −0.27138 −0.27931 Median −0.27173 −0.25626 −0.26456 −0.04339 0.008014 −0.04381 −0.04394 −0.27672 −0.29129 Max −0.20023 −0.20007 −0.20018 34.91703 8.740083 7.182482 13.78985 −0.20023 −0.20086 PCA4 Min −1.17361 −1.13483 −1.21844 −0.39205 −0.38758 −0.39849 −0.39561 −0.36964 −0.38206 Mean −0.85262 −0.83671 −0.8048 0.614565 0.833197 0.600433 0.604744 0.646062 0.758589 Median −0.87973 −0.86109 −0.8269 0.451215 0.567642 0.449885 0.359338 0.523269 0.57825 Max −0.4226 −0.43388 −0.41083 2.809658 3.04613 2.884778 2.972785 2.6186 2.974322 PCA5 Min −0.19829 −0.19924 −0.19297 −1.79801 −2.53365 −2.6192 −2.44086 −2.6779 −2.62344 Mean 0.810572 0.736591 0.728155 −0.72144 −0.84754 −0.80889 −0.82297 −0.72856 −0.70873 Median 0.764994 0.693731 0.657955 −0.72833 −0.77132 −0.70957 −0.77948 −0.59442 −0.57736 Max 2.416623 2.278981 2.616655 −0.20335 −0.20762 −0.20218 −0.20251 −0.20116 −0.20382 Cluster24 Cluster23 (SEQ ID Cluster32 (SEQ ID NO: Cluster25 Cluster26 Cluster27 Cluster28 Cluster29 Cluster30 Cluster31 (SEQ ID NO: 3731--SEQ 3849--SEQ (SEQ ID NO: (SEQ ID NO: (SEQ ID NO: (SEQ ID NO: (SEQ ID NO: (SEQ ID NO: (SEQ ID NO: NO: 5162-SEQ ID ID 3981--SEQ ID 4192--SEQ ID 4401--SEQ ID 4529--SEQ ID 4646--SEQ ID 4836--SEQ ID 5046--SEQ ID ID NO: 3848) NO: 3980) NO: 4191) NO: 4400) NO: 4528) NO: 4645) NO: 4835) NO: 5045) NO: 5161) NO: 5286) PCA1 Min −0.39968 −0.93205 −0.38484 −0.93175 −0.36299 −0.93202 −0.39541 −0.93174 −0.38676 −0.93219 Mean 0.569528 −0.7112 0.89369 −0.71148 0.847871 −0.6997 0.733638 −0.71468 0.713562 −0.72235 Median 0.307897 −0.71444 0.656779 −0.7205 0.473467 −0.71199 0.522102 −0.72051 0.378272 −0.72062 Max 2.76172 −0.40915 3.044789 −0.40213 6.206739 −0.40329 2.997077 −0.40188 2.942702 −0.40344 PCA2 Min −4.50821 −4.32937 0.205796 0.217611 −3.95614 −4.39001 0.203336 0.213622 −3.27891 −4.31097 Mean −0.777 −0.77438 0.615151 0.627195 −0.58233 −0.66813 0.642413 0.668567 −0.54379 −0.6389 Median −0.41811 −0.59493 0.63135 0.641379 −0.23895 −0.27959 0.691753 0.727605 −0.27039 −0.39873 Max 0.196954 0.180603 0.941307 0.956251 0.199442 0.199682 0.947101 0.955864 0.197573 0.197193 PCA3 Min −0.30606 −0.31336 −0.19852 −0.19834 −0.19909 −0.19493 −0.31606 −0.32335 −0.30162 −0.31598 Mean −0.25642 −0.26736 0.171006 0.21757 0.20907 0.183239 −0.26663 −0.28001 −0.25672 −0.27043 Median −0.26139 −0.27169 −0.03015 −0.02662 −0.03223 −0.06903 −0.27011 −0.28811 −0.25858 −0.27998 Max −0.20052 −0.20409 4.462448 7.171082 7.193004 6.524651 −0.20077 −0.20004 −0.20218 −0.20128 PCA4 Min −0.39748 −0.39925 −0.7756 −0.74818 −0.78247 −0.75487 −0.79614 −0.74639 −0.78065 −0.74365 Mean 0.668717 0.649507 −0.63225 −0.6052 −0.61175 −0.59977 −0.62563 −0.61235 −0.62339 −0.59687 Median 0.41274 0.413211 −0.63785 −0.61495 −0.61728 −0.60438 −0.63223 −0.61292 −0.63546 −0.6038 Max 2.854384 2.911189 −0.40047 −0.40417 −0.40476 −0.41372 −0.41488 −0.40099 −0.40756 −0.40546 PCA5 Min −2.18571 −2.49096 −2.21238 −2.21096 −2.21537 −2.20254 −2.39722 −2.17311 −2.11438 −2.35552 Mean −0.85226 −0.79404 −0.8952 −0.956 −0.91416 −0.91719 −0.96664 −0.96062 −0.95439 −0.98418 Median −0.79315 −0.76484 −0.83735 −0.91891 −0.92024 −0.83148 −0.90166 −0.94788 −0.90938 −0.885 Max −0.20566 −0.20015 −0.20978 −0.20039 −0.22084 −0.20408 −0.2077 −0.21493 −0.20199 −0.22725

Example 3: Design of Zinc Fingers to Bind Genomic Loci in Zea mays

Zinc finger proteins directed against the identified DNA sequences of the representative genomic loci were designed as previously described. See, e.g., Urnov et al., (2005) Nature 435:646-551. Exemplary target sequence and recognition helices are shown in Table 7 (recognition helix regions designs) and Table 8 (target sites). In Table 8, nucleotides in the target site that are contacted by the ZFP recognition helices are indicated in uppercase letters and non-contacted nucleotides are indicated in lowercase. Zinc Finger Nuclease (ZFN) target sites were designed for all of the previously described 72 selected genomic loci. Numerous ZFP designs were developed and tested to identify the fingers which bound with the highest level of efficiency with 72 different representative genomic loci target sites which were identified and selected in Zea mays as described above. The specific ZFP recognition helices (Table 7) which bound with the highest level of efficiency to the zinc finger recognition sequences were used for targeting and integration of a donor sequence within the Zea mays genome.

TABLE 7 zinc finger designs for the Zea mays selected genomic loci (N/A indicates “not applicable”). It should be noted that the ZFP recognition helices that are identified with an asterisk (*) were designed for targeting and integration of a donor sequence, but the completion of donor integration within these genomic loci has not been completed. pDAB ZFP Number Number F1 F2 F3 F4 F5 F6 111879 111879ZFN5 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: 5287 NO: 5288 NO: 5289 NO: 5290 NO: 5291 NO: 5292 QSGDL RKDQL RSDDLTR TSSNRKT RSDTLSE ARSTRTN TR VA 111879ZFN7 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: 5293 NO: 5294 NO: 5295 NO: 5296 NO: 5297 NO: 5298 RSDSLSV DRSNR QSSHLTR RSDAL RSDDLTR DPSALRK KT AR 111885 111885ZFN1 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: 5299 NO: 5300 NO: 5301 NO: 5302 NO: 5303 NO: 5304 RSDNLSQ ASNDR ERGTL RSDHLSR ERGTL QSGHLSR KK AR AR 111885ZFN2 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: 5305 NO: 5306 NO: 5307 NO: 5308 NO: 5309 NO: 5310 RSANL DRSDLSR RSDTLSQ RSADLSR DRSNLSR NSRNLRN AR 117404 SIG115737_31v1 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: 5311 NO: 5312 NO: 5313 NO: 5314 NO: 5315 NO: 5316 RSDSLSV DRSHL DRSNLSR RRSDL RSDTLSE QNATRIN AR KR SIG115737_32v1 SEQ ID SEQ ID SEQ ID SEQ ID N/A N/A NO: 5317 NO: 5318 NO: 5319 NO: 5320 QSGSLTR QSGDL RSDVLSE TRNGL TR KY 117408 SIG120523_11v1 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: 5321 NO: 5322 NO: 5323 NO: 5324 NO: 5325 NO: 5326 RSDNLSR DNSNR QNAHR QKATRIT DRSHLTR RSDDRKK KT KT SIG120523_12v1 SEQ ID SEQ ID SEQ ID SEQ ID N/A N/A NO: 5327 NO: 5328 NO: 5329 NO: 5330 ASKTRTN QSGSLTR LRHHL QSAHL TR KA 117400 SIG115246_5 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: 5331 NO: 5332 NO: 5333 NO: 5334 NO: 5335 QSGDL ASHNL DRSNLTR QSSDLSR DAGNR TR RT NK SIG115246_6 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: 5336 NO: 5337 NO: 5338 NO: 5339 NO: 5340 DRSDLSR RSDNLTR DRSHLSR TSGNLTR QSSDLSR 117402 SIG115636_1v1 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: 5341 NO: 5342 NO: 5343 NO: 5344 NO: 5345 NO: 5346 QSSDLSR HRSTR RSDDLTR DRSNL DRSHLTR QRSTLKS NR KA SIG115636_2v1 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: 5347 NO: 5348 NO: 5349 NO: 5350 NO: 5351 NO: 5352 RSDALSR RSDDLTR DRSHLTR TSSNRKT RSDTLSE DRSHLAR 117406 SIG120417_11v1 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: 5353 NO: 5354 NO: 5355 NO: 5356 NO: 5357 NO: 5358 DRSAR QSGHLSR QSGNL RSDVLST RYAYL RRWTLVG TR AR TS SIG120417_12v1 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: 5359 NO: 5360 NO: 5361 NO: 5362 NO: 5363 RSDNLSQ ASNDR QSGDL LKDTL QSGNL KK TR RR AR 117411 SIG120621_15v1 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: 5364 NO: 5365 NO: 5366 NO: 5367 NO: 5368 QSGDL MQNYL RSDHLSE QNANR RSADLTR TR SR KT SIG120621_16v1 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: 5369 NO: 5370 NO: 5371 NO: 5372 NO: 5373 NO: 5374 RSDNLSE QSANR RSDALSR DRSAL RSDHLSE DSQNRIK TK AR 117413 SIG12078_11v1 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: 5375 NO: 5376 NO: 5377 NO: 5378 NO: 5379 NO: 5380 QSGDL DKGNL RSADLTR DRSHL RSDTLSE DRSNRKT TR TK AR SIG12078_12v1 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: 5381 NO: 5382 NO: 5383 NO: 5384 NO: 5385 NO: 5386 DRSNLSR LRQDL RSDHLSE DRSAL DRSALSR NRRGRWS KR AR 117429 SIG157315_1v1 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: 5387 NO: 5388 NO: 5389 NO: 5390 NO: 5391 NO: 5392 RPYTLRL HRSSLRR RSDSLLR WLSSLSA QSGDL DRSHLAR TR SIG157315_2v1 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: 5393 NO: 5394 NO: 5395 NO: 5396 NO: 5397 DRSNLSR LKQHL LRHHL QSGNL TSGHLSR NE TR HV 124802 SEQ ID SEQ ID SEQ ID SEQ ID N/A N/A NO: 5495 NO: 5496 NO: 5497 NO: 5498 QSSDLSR QSGNL DRSNR DNSNRIK AR TT SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: 5499 NO: 5500 NO: 5501 NO: 5502 NO: 5503 QSSDLSR RTDAL RSDHLSE SYRSR DRSAL RG WG AR 121900 SIGPPL05_1 SEQ ID SEQ ID SEQ ID SEQ ID N/A N/A NO: 5504 NO: 5505 NO: 5506 NO: 5507 RSDTLSE QSGDL TSGNLTR DRSAL TR AR SIGPPL05_2 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: 5508 NO: 5509 NO: 5510 NO: 5511 NO: 5512 NO: 5513 RSDSLSV QSGDL DRSNLSR RQDSRSQ RSDHLSA QHGSLAS TR 124810 SIGPPL06_9 SEQ ID SEQ ID SEQ ID SEQ ID N/A N/A NO: 5514 NO: 5515 NO: 5516 NO: 5517 RSANL RSDHLTT RSANL TNQNRIT AR AR SIGPPL06_10 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: 5518 NO: 5519 NO: 5520 NO: 5521 NO: 5522 QSGNL QSNQL QNAHR RSDDLSK RSDTR AR AV KT KT 121902 SIGPPL07_1 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: 5523 NO: 5524 NO: 5525 NO: 5526 NO: 5527 NO: 5528 QSSHLTR QSSDLTR RSDDLTR QSSDLRR TSGSLSR TSSNRAV SIGPPL07_2 SEQ ID SEQ ID SEQ ID SEQ ID N/A N/A NO: 5529 NO: 5530 NO: 5531 NO: 5532 RSDHLSR DRSAR RSDTLSE SRCWR NS RK 123802 ZmPPL18SIG_5 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: 5533 NO: 5534 NO: 5535 NO: 5536 NO: 5537 NO: 5538 TSGNLTR LKQML QSSNLAR RSDNLTR RSDNLST QSGHLSR AV ZmPPL18SIG_6 SEQ ID SEQ ID SEQ ID SEQ ID N/A N/A NO: 5539 NO: 5540 NO: 5541 NO: 5542 RSDNL QKKDR RSDVLSR DSRDR AR SY KN 123805 ZmSIGPPL19_1 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: 5543 NO: 5544 NO: 5545 NO: 5546 NO: 5547 RSAHLSR QSANR QSSDLSR QSSDLSR QWSTR TK KR ZmSIGPPL19_2 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: 5548 NO: 5549 NO: 5550 NO: 5551 NO: 5552 NO: 5553 QSSDLSR QSAHR RSDNLST DSSTRKT RSDHLSR DRSNRKT KN 121992 ZmPPL20v2_1 SEQ ID SEQ ID SEQ ID SEQ ID N/A N/A NO: 5554 NO: 5555 NO: 5556 NO: 5557 QSSDLSR QAGNL DRSNLSR LKQHL SK TR ZmPPL20v2_2 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: 5558 NO: 5559 NO: 5560 NO: 5561 NO: 5562 DRSNLSR QSGDL QSSDLSR QAGNL QNAHR TR SK KT 118643 SIGPPL09_1 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: 5563 NO: 5564 NO: 5565 NO: 5566 NO: 5567 NO: 5568 RSDHLSQ QNAHRIT RSDDLTR QRSTLSS TSGNLTR DRSNLTR SIGPPL09_2 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: 5569 NO: 5570 NO: 5571 NO: 5572 NO: 5573 NO: 5574 TSGNLTR RSDDLTR QSGDL MQNYL QSGNL DQSGLAH TR SR AR 118648 SIGPPL10_5 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: 5575 NO: 5576 NO: 5577 NO: 5578 NO: 5579 NO: 5580 rsdnlst drsalar lkqhltr rrddlrn rsddltr drsnlka SIGPPL10_6 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: 5581 NO: 5582 NO: 5583 NO: 5584 NO: 5585 NO: 5586 rsdtlse qsgdltr qsgdltr drsvlrr rsdnlar drsnltr 118650 SIGPPL21_1 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: 5587 NO: 5588 NO: 5589 NO: 5590 NO: 5591 DRSHLTR QSGDL QSGDL RSDNLSE KRGNR TR TR AK SIGPPL21_2 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: 5592 NO: 5593 NO: 5594 NO: 5595 NO: 5596 NO: 5597 ERGTL RSDAL RSDALSR DRSAL ERGTL DRSALAR AR AR AR AR 118654 SIGPPL22_3 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: 5598 NO: 5599 NO: 5600 NO: 5601 NO: 5602 QSSDLSR RSDHLSR RSDTLSQ QKATRIT RSDAL AR SIGPPL22_4 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: 5603 NO: 5604 NO: 5605 NO: 5606 NO: 5607 RSDNLSV DRSHL RSDTLSR QSADR TSGHLSR AR TK 118656 SIGPPL23_1 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: 5608 NO: 5609 NO: 5610 NO: 5611 NO: 5612 NO: 5613 QRSNL DRSHL RSDTLSE RMYTL DRSALSR RSDDLTR VR AR SK SIGPPL23_2 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: 5614 NO: 5615 NO: 5616 NO: 5617 NO: 5618 RSDALTQ DRSDLSR RRTDL RSDNL QRSPLPA RR AR 118659 SIGPPL24_4 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: 5619 NO: 5620 NO: 5621 NO: 5622 NO: 5623 NO: 5624 RSDSLSA QNAHR ERGTL RSDNLTR TSGNLTR QRSHLSD KT AR SIGPPL24_3 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: 5625 NO: 5626 NO: 5627 NO: 5628 NO: 5629 NO: 5630 QSGDL QRSNL RSDNL DRSVL DRSDLSR RQDTLRS TR NI AR HR 118660 SIGPPL25_2 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: 5631 NO: 5632 NO: 5633 NO: 5634 NO: 5635 NO: 5636 RSDALSR QSGSLTR RSDALSV DSSHRTR QSGDL QSGHLSR TR SIGPPL25_1 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: 5637 NO: 5638 NO: 5639 NO: 5640 NO: 5641 NO: 5642 RSDNL HRNTL TSGSLSR RSDHLTT QSGDL RPYTLRL AR LG TR 118767 SIGPPL26_1 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 5643 5644 5645 5646 5647 RSADLTR RSDAL RSDTLSQ RSDDR TSGSLSR AR KK SIGPPL26_2 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 5648 5649 5650 5651 5652 RSDTLSA RSADR QRSNL DRSHL RSDALSV KK VR AR 118769 SIGPPL27_1 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 5653 5654 5655 5656 5657 DRSNLSR QSGNL RSDHLTQ QSGDL LRHQL AR TR KS SIGPPL27_2 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: NO: NO: NO: NO: NO: 5663 5658 5659 5660 5661 5662 TTRYRNR RSADLTR QSGDL DRSHLSR TSGNLTR RSDHLSA TR 118663 SIGPPL28_1 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 5664 5665 5666 5667 5668 QSSDLSR QSGSLTR QSGHLSR TSGNLTR QSGHLSR SIGPPL28_2 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 5669 5670 5671 5672 5673 QSGNL DISNRSK DRSDLSR RRTDL TSGSLTR AR RR 118668 SIGPPL29_5 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 5674 5675 5676 5677 5678 DRSHLSR TSGNLTR DRSNLSR FPGSRTR RNDDR KK SIGPPL29_6 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: NO: NO: NO: NO: NO: 5684 5679 5680 5681 5682 5683 DNSNRKT TSGSLSR QLNNL RSDVLST ASGNL RSDNLSR KT LN 118669 SIGPPL30_1 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: NO: NO: NO: NO: NO: 5690 5685 5686 5687 5688 5689 QSGHLSR RSDTLSQ ASANR QSSNLAR DSSDR RSDHLST TK KK SIGPPL30_2 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 5691 5692 5693 5694 5695 RSDHLSA SYWSR DRSALSR DRSHL RSDNLTR TV AR 118670 SIGPPL31_1 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 5696 5697 5698 5699 5700 DRSDLSR DRSNR RSDVLSE RNFSLTM RSDAL NK AR SIGPPL31_2 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 5701 5702 5703 5704 5705 QSGAL QSSDLSR RRDILHQ RSADLTR QSGDL AR TR 118673 SIGPPL32_5 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 5706 5707 5708 5709 5710 QSGAL DRSNLSR LKQHL RSDNLST RSDHLSR AR TR SIGPPL32_6 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 5711 5712 5713 5714 5715 QSSDLSR HRSNL DRSNLSR DASNL TSSNLSR NK RQ 118674 SIGPPL33_1 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NA NO: NO: NO: NO: NO: 5716 5717 5718 5719 5720 RSDSLLR CREYR TSGHLSR RSDVLSA RNDHRIN GK SIGPPL33_2 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: NO: NO: NO: NO: NO: 5726 5721 5722 5723 5724 5725 DRSTRIT QSGSLTR RSDNL QSGSLTR RLDNR RSDVLSN RE TA 118676 SIGPPL34_1 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: NO: NO: NO: NO: NO: 5732 5727 5728 5729 5730 5731 QSGHLSR RSDSLLR WLSSLSA ERGTL TSGSLTR RSDTLSE AR SIGPPL34_2 SEQ ID SEQ ID SEQ ID SEQ ID N/A N/A NO: NO: NO: NO: 5733 5734 5735 5736 QSGNL DISNRSK RSDHLSR HRYHR AR LS 118677 SIGPPL35_1 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: NO: NO: NO: NO: NO: 5742 5737 5738 5739 5740 5741 HKYHLRS QSGSLTR DRSHL DRSALSR RSDAL QSSDLSR AR AR SIGPPL35_2 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: NO: NO: NO: NO: NO: 5748 5743 5744 5745 5746 5747 RSDHLTT RSDHLSE RKDARIT ERGTL RSDALTQ DRSHLTR AR 118680 SIGPPL36_1 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 5749 5750 5751 5752 5753 TSGSLSR QMHHL TSSNLSR QSGAL RSDDLTR KT AR SIGPPL36_2 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: NO: NO: NO: NO: NO: 5759 5754 5755 5756 5757 5758 ARSTRTN DRSALSR RSDHLSR DRSAR QSGHLSR RSDHLSE TR 118683 SIGPPL37_1 SEQ ID SEQ ID SEQ ID SEQ ID N/A N/A NO: NO: NO: NO: 5760 5761 5762 5763 RSANL RNDDR DRSHLTR DRSNLTR AR KK SIGPPL37_2 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 5764 5765 5766 5767 5768 TSGSLSR DSSDR QSGDL DRSHLTR DRSHL KK TR AR 118685 SIGPPL38_1 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 5769 5770 5771 5772 5773 RSDHLSA TKSNRTK DRSNLTR RSDDLTR QKSSLRT SIGPPL38_2 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: NO: NO: NO: NO: NO: 5779 5774 5775 5776 5777 5778 HRRSRWG RREDLIT TSSNLSR DRSALSR RSDDR RSDTLSE KT 123833 ZmSIGPPL39_1 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: NO: NO: NO: NO: NO: 5785 5780 5781 5782 5783 5784 HKYHLRS RSDNLSA RNNDR QSGDL RSDDLTR QSSDLSR KT TR ZmSIGPPL39_2 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: NO: NO: NO: NO: NO: 5791 5786 5787 5788 5789 5790 HRKSLSR TNQNRIT HRSSLRR DSSTRKT QSATRTK QSSDLSR 118771 SIGPPL40_1 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 5792 5793 5794 5795 5796 QSSDLSR QSTHR RSDHLTQ DRSDLSR RSDNLTR NA SIGPPL40_2 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 5797 5798 5799 5800 5801 QSGDL DRSHLTR QSGSLTR DRSNLSR QSGNL TR AR 121943 ZmSIGPPL41_7 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: NO: NO: NO: NO: NO: 5807 5802 5803 5804 5805 5806 DNSNRIN DRSALSR RSDALTQ RSDSLLR RSDALTQ RSDNLST ZmSIGPPL41_8 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: NO: NO: NO: NO: NO: 5813 5808 5809 5810 5811 5812 TSSNRKT RSDNLST RSDNR RSDVLST WSSSR QSGSLTR TK AA 121946 ZmSIGPPL42_7 SEQ ID SEQ ID SEQ ID SEQ ID N/A N/A NO: NO: NO: NO: 5814 5815 5816 5817 QSSHLTR RSDALTQ ERGTL RNDDR AR KK ZmSIGPPL42_8 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: NO: NO: NO: NO: NO: 5823 5818 5819 5820 5821 5822 RSDDLTR QSGSLTR TSSNRKT RSDNLSV QNANRIT ERGTL AR 121949 ZmSIGPPL43_3 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: NO: NO: NO: NO: NO: 5829 5824 5825 5826 5827 5828 TSGSLTR RSDNLSE RHSALSA QSSDLSR QSYNR ERGTL FV AR ZmSIGPPL43_4 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 5830 5831 5832 5833 5834 ERGTL RSDDLTR RSDHLSE RNQHR DRSHL AR KN AR 121952 ZmSIGPPL44_1 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 5835 5836 5837 5838 5839 QSGNL QGANLIK RSDSLSV DRSDLSR QSGHLSR AR ZmSIGPPL44_2 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 5840 5841 5842 5843 5844 TSGSLSR QSGSLTR RSAHLSR RSDALST DRSTRTK 121959 ZmSIGPPL45_7 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 5845 5846 5847 5848 5849 RSDDLSK QSATRTK RSDALTQ DRSHLTR TSSNRKT ZmSIGPPL45_8 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: NO: NO: NO: NO: NO: 5855 5850 5851 5852 5853 5854 DCRNRWR DRSALSR TSSNRKT RSADLTR RSDDLTR RSDVLST 121963 ZmSIGPPL46_7 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 5856 5857 5858 5859 5860 QSSDLSR QSGSLTR QSSDLSR RSDNLST RSDNR TK ZmSIGPPL46_8 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: NO: NO: NO: NO: NO: 5866 5861 5862 5863 5864 5865 RSADRKK QSSDLSR AASNR DRSHLSR DRSHL RSDTLSA SK AR 121971 ZmSIGPPL48_7 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 5867 5868 5869 5870 5871 RSDNLST DRSNR RSDAL RSDNLST DRSAL KT AR AR ZmSIGPPL48_8 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: NO: NO: NO: NO: NO: 5877 5872 5873 5874 5875 5876 TRSPLTT DRSDLSR DRSNR QSSDLSR WRSSL RSDHLSQ NK RQ 121972 ZmSIGPPL49_1 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 5878 5879 5880 5881 5882 TRDHLST RSDAR RSDHLSE QSNHR RSDAL TN KT AR ZmSIGPPL49_2 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: NO: NO: NO: NO: NO: 5888 5883 5884 5885 5886 5887 QSADRTK ERGTL RSDALTQ RSDSLSV DRSAL QSSNLAR AR AR 124097 ZmSIGPPL50_5 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 5889 5890 5891 5892 5893 RSDHLSA QSGDL QSSDLSR RSDNL FREGLYK TR AR ZmSIGPPL50_6 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: NO: NO: NO: NO: NO: 5899 5894 5895 5896 5897 5898 QSSDLTR TSGNLTR LKQML ERGTL RSDHLSR QSSHLTR AV AR 123818 ZmPPL51_7 SEQ ID SEQ ID SEQ ID SEQ ID N/A N/A NO: NO: NO: NO: 5900 5901 5902 5903 RSDTLSE HRRSR RSDDLSV TSSNRTK WG ZmPPL51_8 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: NO: NO: NO: NO: NO: 5909 5904 5905 5906 5907 5908 WLSSLSA RSDTLSQ QRDHRIK DRSNLSR TSGNLTR RSDSLLR 118705 SIGPPL52_5 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 5910 5911 5912 5913 5914 DRSNLSR LRQNLIM QNAHR QSGAL QSGHLSR KT AR SIGPPL52_6 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: NO: NO: NO: NO: NO: 5920 5915 5916 5917 5918 5919 DSSDRKK QSGNL LAYDR RSDVLSE RNFSLTM RSADLTR AR RK 118711 SIGPPL54_5 SEQ ID SEQ ID SEQ ID SEQ ID N/A N/A NO: NO: NO: NO: 5921 5922 5923 5924 RSDNL DQSYR RSDNLSE TSSNRKT AR RT SIGPPL54_6 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: NO: NO: NO: NO: NO: 5930 5925 5926 5927 5928 5929 RSDYLAK TSGSLSR RKELLRS RPYTLRL HRSSLRR DRSTRTK 118718 ZmSIGPPL57_1 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: NO: NO: NO: NO: NO: 5936 5931 5932 5933 5934 5935 QSGNLAR QSSDLSR QSTHR RSADLTR RSDDLTR DRSNLSR NA ZmSIGPPL57_2 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 5937 5938 5939 5940 5941 QSGHL DRSHL RSANL QSANR RSDHLTQ AR AR AR TK 118722 ZmSIGPPL58_3 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 5942 5943 5944 5945 5946 QSSDLSR RSDHLTQ DRSAL RSDYL QSGDL AR AK TR ZmSIGPPL58_4 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: NO: NO: NO: NO: NO: 5952 5947 5948 5949 5950 5951 RSDNLTT RSDNLSQ QRQHR DQSNL RPYTLRL QSSNLAR KT RA 118726 SIGPPL59_5 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 5953 5954 5955 5956 5957 QSGHL QRVAL ERGTL QSGDL RSDDLTR AR QA AR TR SIGPPL59_6 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 5958 5959 5960 5961 5962 QSSDLSR HRSNL RSADLTR TNQNRIT RSDAL NK AR 118728 ZmSIGPPL60_3 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: NO: NO: NO: NO: NO: 5968 5963 5964 5965 5966 5967 RSDNLTR DSSALIN TSSNLSR RSDHLSR YGWYR TSGHLSR HK ZmSIGPPL60_4 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 5969 5970 5971 5972 5973 QSGHL QRTNL DRSTRTK QSGNL RSDHLTQ AR VE HV 118732 SIGPPL61_5 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 5974 5975 5976 5977 5978 RSDNLST RSDNR RSDNL QKVNL QSGAL TK AR MS AR SIGPPL61_6 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 5979 5980 5981 5982 5983 QSGDL TQGYL RSDNL DSSGLTH RNDDR TR RK AR KK 118733 ZmSIGPPL62_1 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: NO: NO: NO: NO: NO: 5989 5984 5985 5986 5987 5988 QSGDLTR DRSDLSR RRDYL RSDTLSE NNRDR RSDTLSE RT TK ZmSIGPPL62_2 SEQ ID SEQ ID SEQ ID SEQ ID N/A N/A NO: NO: NO: NO: 5990 5991 5992 5993 QSSDLSR QSTHR RSDDLSK RSDAL NA AR 118735 SIGPPL62_5 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: NO: NO: NO: NO: NO: 5999 5994 5995 5996 5997 5998 QSTPLFA RSANL RSDDLTR RSDALST DRSTRTK QSGNL AR AR SIGPPL62_6 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 6000 6001 6002 6003 6004 QSGHL ERIALVR RSDHLSE RSAHLSR RSDNLSV AR 118739 ZmSIGPPL64_1 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 6005 6006 6007 6008 6009 RSDTLSE QSHNR DRSHLTR DRSAL TSGSLTR TK AR ZmSIGPPL64_2 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: NO: NO: NO: NO: NO: 6015 6010 6011 6012 6013 6014 RSDNLTR LRHHL QSYAR RSDNLST RSDDLTR RSAHLSR TR TL 118742 SIGPPL65_1 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 6016 6017 6018 6019 6020 RSDDLSK DRSNR DRSNLSR QRTHL QSGHLSR KT RD SIGPPL65_2 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 6021 6022 6023 6024 6025 QSSDLSR QSGNR DRSNLTR QSGHL QRTNL TT AR VE 118745 ZmSIGPPL66_1 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 6026 6027 6028 6029 6030 QSGDL RRDPLIN QSGDL RSDSLSR DKSNRIK TR TR ZmSIGPPL66_2 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 6031 6032 6033 6034 6035 QSSDLSR QSGDL QSSDLSR TSGNLTR QTSDR TR NK 124081 ZmSIGPPL67_3 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 6036 6037 6038 6039 6040 QSGSLTR RNDDR RSDSLSA QNAHR QNAHR KK KT KT ZmSIGPPL67_4 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 6041 6042 6043 6044 6045 QSGDL DKGNL QSSDLSR QSAHR QSSDLSR TR TK KN 125361 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: NO: NO: NO: NO: NO: 6051 6046 6047 6048 6049 6050 DRSHLAR RSDALSR QSGSLTR QSGSLTR QSGSLTR TSGHLSR SEQ ID SEQ ID SEQ ID SEQ ID N/A N/A NO: NO: NO: NO: 6052 6053 6054 6055 QSGDL RSDHLSR RSDHLST RSDHLSR TR 118753 SIGPPL69_5 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 6056 6057 6058 6059 6060 QSSDLSR RSDYL QSGDL LRQTL QSGHLSR RK TR NS SIGPPL69_6 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 6061 6062 6063 6064 6065 RSDTLSV DNSTRIK RSDNLST DNSNRIN TSSNLSR 124878 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 6066 6067 6068 6069 6070 RSDVLSA QNATRIN RSDVLSE QSGNL RSDNLSV AR SEQ ID SEQ ID SEQ ID SEQ ID N/A N/A NO: NO: NO: NO: 6071 6072 6073 6074 QSADR DRSNLTR RSDNLSE KRCNL TK RC 123829 ZmSIGPPL71_5 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: NO: NO: NO: NO: NO: 6080 6075 6076 6077 6078 6079 QRSNLDS DRSNLSR DSSAR TSGNLTR DRSNLTR DRSNLSR NT ZmSIGPPL71_6 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 6081 6082 6083 6084 6085 QSGNL QKVNR RSDNLSV QRNHR QKATRIT AR AG TT 118761 ZmSIGPPL72_3 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: NO: NO: NO: NO: NO: 6091 6086 6087 6088 6089 6090 TSSDRTK QSGAL LRHNL DRSTRTK HRSAR RSDHLSE AR RA KR ZmSIGPPL72_4 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 6092 6093 6094 6095 6096 RSDSLSR DKSNRIK RSDDLTR DRSHLTR DRSNLTR 121904 SIGPPL74_1 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 6097 6098 6099 6100 6101 RSDNLST RQWSL TSGHLSR QSSDLSR RSDDLTR RI SIGPPL74_2 SEQ ID SEQ ID SEQ ID SEQ ID N/A N/A NO: NO: NO: NO: 6102 6103 6104 6105 RSANL RLDNR QSGHL DSSNREA AR TA AR 121905 ZmSIGPPL75_1 SEQ ID SEQ ID SEQ ID SEQ ID N/A N/A NO: NO: NO: NO: 6106 6107 6108 6109 RSDALSR RSDNLTR RSADLTR RSDNLTR ZmSIGPPL75_2 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 6110 6111 6112 6113 6114 RSDNLSV RSDTRTE TSGSLSR QSGNL RSADLTR AR 121917 SIGPPL76_2 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: NO: NO: NO: NO: NO: 6120 6115 6116 6117 6118 6119 QSGHLSR TSGSLSR RSDHLTE RSDDLTR QRSTLS ERGTL AR SIGPPL76_1 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: NO: NO: NO: NO: NO: 6126 6121 6122 6123 6124 6125 DKANRTR RSDHLSQ DNASRIR RSDNLST AQWTR RSDHLSE AC 121918 ZmSIGPPL77_2 SEQ ID SEQ ID SEQ ID SEQ ID N/A N/A NO: NO: NO: NO: 6127 6128 6129 6130 QSSDLSR LRHNL RSDTLST DRSSRIK RA ZmSIGPPL77_1 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: NO: NO: NO: NO: NO: 6136 6131 6132 6133 6134 6135 DSSTRRR QSGAL RSDNLTR RSDNLST DRSNLTR DRSDLSR AR 121909 SIGPPL78_1 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 6137 6138 6139 6140 6141 DRSAL DRSALSR DRSHL RSDNLST RSDAR AR AR AN SIGPPL78_2 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 6142 6143 6144 6145 6146 RSDHLST DSSNRIK QSGAL RSDDLTR QSGSLTR AR 121912 SIGPPL79_1 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: NO: NO: NO: NO: NO: 6152 6147 6148 6149 6150 6151 HSNARKT DRSHLSR DRSHL QSSDLSR QSGDL RSDNLSE AR TR SIGPPL79_2 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: NO: NO: NO: NO: NO: 6158 6153 6154 6155 6156 6157 TSANLSR RSDALSV DSSHRTR QSGDL ASHNL RSDHLST TR RT 121981 ZmSIGPPL80_3 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: NO: NO: NO: NO: NO: 6164 6159 6160 6161 6162 6163 TSGNLTR DRSDLSR DRSNLTR RSDSLLR RLDWL RSADLTR PM ZmSIGPPL80_4 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 6165 6166 6167 6168 6169 RSDNLSQ DRSNR DSSDR RSDHLSE QSASR TK KK KN 124091 ZmSIGPPL81_3 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 6170 6171 6172 6173 6174 RSDVLST STAALSY QSANR QNAHR QSSDLSR TT KT ZmSIGPPL81_4 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 6175 6176 6177 6178 6179 QRNHR DRSNLTR TSGNLTR QSNQL RSDALTQ TT RQ 127268* SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 6620 6621 6622 6623 6624 DRSAL DYYGR DRSHL YRSSLKE TSGNLTR AR HG AR SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: NO: NO: NO: NO: NO: 6630 6625 6626 6627 6628 6629 HRSSLRR HHHVL QNATR DRSTRTK RRDNL QKATR VQ TK HS TT 120993* SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: NO: NO: NO: NO: NO: 6636 6631 6632 6633 6634 6635 FRGSLTW QSSDLSR QWSTR RSDVLSE QTVHR RSDTLSE KR NS SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 6637 6638 6639 6640 6641 RSDNLST RSTHRTQ RSDNLSV QKATRIN DRSNLTR 228254* SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: NO: NO: NO: NO: NO: 6647 6642 6643 6644 6645 6646 RSDNLTR QSGNL CRQNL DRSNLSR DGRNL RSDHLST AR AN RH SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: NO: NO: NO: NO: NO: 6653 6648 6649 6650 6651 6652 YRSNLVR DRSNR QNATRIN QSGNL HKLSLSI DRSDLSR TT AR 200497* SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 6654 6655 6656 6657 6658 DRSALSR QSGSLTR RSDNLTR RQDCL RNDNR SL KT SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 6659 6660 6661 6662 6663 QSGNL DQSGL QSANR DRSDLSR RSHHL AR AH TK KA  66202* SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 6664 6665 6666 6667 6668 QSGNL QSGSLTR DRSALSR QSGSLTR QSGNL AR AR SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: NO: NO: NO: NO: 6669 6670 6671 6672 6673 QSGNL WRISLAA RSDNLSE RSQHR QSSDLSR AR KT  5607* SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: NO: NO: NO: NO: NO: 6679 6674 6675 6676 6677 6678 LKHHLTD RSANL RSDHLTT RSDNLSE DRSHL QSAHR AR AR KN SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: NO: NO: NO: NO: NO: 6685 6680 6681 6682 6683 6684 DSSNLAT TSGNLTR DRSNLTR RSDNLSQ RKADR TSGNLTR TK

TABLE 8 Zinc finger target site of Zea mays selected genomic loci pDAB ZFP Number and SEQ Locus ID Name Number Binding Site (5′ → 3′) ID NO: optimal_loci_204637 OGL1 111879 111879ZFN5: 5398 ctACTCCGTATGCGAAGGCAcg 111879ZFN7: 5399 taTTCGCGGTGGGACACTTGat optimal_loci_204726 OGL2 111885 111885ZFN1: 5400 ccGGAGCCGGGGCCTCCCAGgc 111885ZFN2: 5401 atCGCGACGCGACGcGACGAGac optimal_loci_156393 OGL12 117404 SIG115737_31v1: 5402 TGCATGCGCAGTA SIG115737_32v1: 5403 ACACCGGCGCACGGCACG optimal_loci_198387 OGL15 117408 SIG120523_11v1:  5404 AGAGGTGTAACC SIG120523.12v1: 5405 TCGGGCACAAGAAACGAG optimal_loci_31710 OGL08 117400 SIG115246_5: 5406 TACGCTGACAATGCA SIG115246_6:  5407 CCAGCTGATGGAGAGGAC optimal_loci_64542 OGL11 117402 SIG115636_1v1: 5408 AGAGCAGGCGAG SIG115636_2v1:  5409 AGCAAAGTGAGTAGTT optimal_loci_197372 OGL14 117406 SIG120417_11v1: 5410 TGGATGGAAGGAATC SIG120417_12v1: 5411 GAAGCTACATCCCAG optimal_loci_232228 OGL16 117411 SIG12062l_15v1: 5412 TACGCGCAACGGAACGCA SIG12062l_16v1: 5413 CACCGGTGTCGTGTAACAG optimal_loci_285621 OGL17 117413 SIG12078_11v1: 5414 CCCGGACGACGCCGAG SIG12078_12v1: 5415 GACATGGCACGCGCATCGAG optimal_loci_157315 OGL13 117429 SIG157315_1v1: 5416 GCATGTGTGGTTTTG SIG157315_2v1: 5417 GGTCAAGGTAGTGAC optimal_loci_43577 OGL04 124802 ZFN_binding_1: 6180 AGCTTCAATAGTA ZFN_binding_2: 6181 GTCTTCCGGTTGGCT optimal_loci_301774 OGL05 121900 ZFN_binding_3: 6182 GTCGATGCACCG ZFN_binding_4: 6183 CTAAGGATGGACGCAGTG optimal_loci_232222 OGL06 124810 ZFN_binding_5: 6184 CATGAGAGGGAT ZFN_binding_6: 6185 ATGTCGTAGAAAAGAA optimal_loci_203704 OGL07 121902 ZFN_binding_7: 6186 CATGTTCGCTGCGGCTGGA ZFN_binding_8: 6187 AGTCCGCTCGGG optimal_loci_59517 OGL09 118643 ZFN_binding_9: 6188 GACGATCTAGCGAGAAGG ZFN_binding_10: 6189 ATCGAAGAACGCAGCGGAT optimal_loci_25001 OGL10 118648 ZFN_binding_12: 6190 CACGCGCCGGGTGTCTAG ZFN_binding_13: 6191 GACGAGCACCGCCCCACCG optimal_loci_112632 OGL18 123802 ZFN_binding_14: 6192 CGGGTACTGGGAAAGGAG ZFN_binding_15: 6193 GAGCGTCCTGATTGACATG optimal_loci_28905 OGL19 123805 ZFN_binding_16: 6194 ACGGTGCATCAAGCTTAAG ZFN_binding_17: 6195 CAAGGGACCTAGTGAGCT optimal_loci_129164 OGL20 121992 ZFN_binding_18: 6196 GGTGACTAAGCT ZFN_binding_19: 6197 AGATAAGCTGCAGAC optimal_loci_2425 OGL21 118650 ZFN_binding_20: 6198 GAGCAGGCAGGCAGGC ZFN_binding_21: 6199 GTCGTCGTCGTGCGTGGCC optimal_loci_122036 OGL22 118654 ZFN_binding_22: 6200 GTGGCAACGGGGGCT ZFN_binding_23: 6201 GGTTCAGCGGGCTAG optimal_loci_5735 OGL23 118656 ZFN_binding_24: 6202 GCGGTCTTGCCGGGCGAA ZFN_binding_25: 6203 CTAGAGGCGCCCATG optimal_loci_178978 OGL24 118659 ZFN_binding_26: 6204 ACGGACAGCCGAGAAAGCA ZFN_binding_27: 6205 CGAGATCGAGGCCAGATCG optimal_loci_288388 OGL25 118660 ZFN_binding_28: 6206 TTGCCATGGGTTATTGAG ZFN_binding_29: 6207 GGAGCATGGCCAGGTAGTG optimal_loci_60310 OGL26 118767 ZFN_binding_30: 6208 CCAGTTCCGACGAGTGGCG ZFN_binding_31: 6209 GGCCTGGGCGAACGCCGCCG optimal_loci_243330 OGL27 118769 ZFN_binding_32: 6210 AGTGCAAGGGAAGAC ZFN_binding_33: 6211 AGGAGGGATGGAGCAGCG optimal_loci_127038 OGL28 118663 ZFN_binding_34: 6212 GGAGATAGGAGTAGCT ZFN_binding_35: 6213 GTTGCGCCCTACGAA optimal_loci_262784 OGL29 118668 ZFN_binding_36: 6214 TCGGTTGACCGATGGC ZFN_binding_37: 6215 AACGAGCCATATGCAAGTT optimal_loci_344662 OGL30 118669 ZFN_binding_38: 6216 GGATGGCTCCGAATGATATG ZFN_binding_39: 6217 GAGGGCGTCTTGAGG optimal_loci_153894 OGL31 118670 ZFN_binding_40: 6218 GTGTTGCTGTACGAC ZFN_binding_41: 6219 GCAGCGAACGGCTGTA optimal_loci_28771 OGL32 118673 ZFN_binding_42: 6220 GGGTAGGGGTGACGTA ZFN_binding_43: 6221 GATCACGACATATCCA optimal_loci_1098 OGL33 118674 ZFN_binding_44: 6222 TGGGTGGGTTTGCGTG ZFN_binding_45: 6223 CCCATGCAGGTAAAGGTA optimal_loci_97772 OGL34 118676 ZFN_binding_46: 6224 GGACTGGGTGCCTGTGTG ZFN_binding_47: 6225 CGTGGGTACGAA optimal_loci_236662 OGL35 118677 ZFN_binding_48: 6226 CGTGCTGTGGTCTGGCGTA ZFN_binding_49: 6227 TGGGGCTATGGCCATGGGG optimal_loci_139485 OGL36 118680 ZFN_binding_50: 6228 GCGGTACGATAGTGTT ZFN_binding_51: 6229 ACTCGGGGAGTCGGGGTC optimal_loci_301175 OGL37 118683 ZFN_binding_52: 6230 GACGGATCGGAG ZFN_binding_53: 6231 GGCGGATGCATCCGTT optimal_loci_152337 OGL38 118685 ZFN_binding_54: 6232 ATAGCGGACCGATCGG ZFN_binding_55: 6233 ATCCCGGCCGGTCGATTCG optimal_loci_202616 OGL39 123833 ZFN_binding_56: 6234 cgtgcttgcggcaccgcag ZFN_binding_57: 6235 gccgctgcacccgttcat optimal_loci_282323 OGL40 118771 ZFN_binding_58: 6236 GAGGACAGGCGAGCT ZFN_binding_59: 6237 GAAGACGTAGGCGCA optimal_loci_262782 OGL41 121943 ZFN_binding_60: 6238 CACAAGATGGTGATGGTC ZFN_binding_61: 6239 CATGTATGTATGTAGTAG optimal_loci_236455 OGL42 121946 ZFN_binding_62: 6240 TCGGCCATGGGA ZFN_binding_63: 6241 GCGGCCAAAAAGCATGTA optimal_loci_162531 OGL43 121949 ZFN_binding_64: 6242 GGTGCCAAAGCCATGCAG ZFN_binding_65: 6243 GGCTGGCGGGCGGCC optimal_loci_344663 OGL44 121952 ZFN_binding_66: 6244 GGAGACTCGATAAGAA ZFN_binding_67: 6245 GCCATGTGGGGTAGTT optimal_loci_337001 OGL45 121959 ZFN_binding_68: 6246 CATGGCATGGCATCG ZFN_binding_69: 6247 CACATGCGCGGCGCATGTC optimal_loci_238100 OGL46 121963 ZFN_binding_70: 6248 TAGTAGGCTAGTAGCT ZFN_binding_71: 6249 ACGCCGCGGCGGCTTGCGCT optimal_loci_264359 OGL48 121971 ZFN_binding_72: 6250 ATCTAGGTGCAACTAG optimal_loci_282653 OGL49 121972 ZFN_binding_73: 6251 GTGAAACGGATGTGT ZFN_binding_74: 6252 TCAGAATATCATGATGGCC optimal_loci_80282 OGL50 124097 ZFN_binding_75: 6253 TGCGAGCGCTGCATGG ZFN_binding_76: 6254 GCTGGAGGGGCCAATGAT optimal_loci_291068 OGL51 123818 ZFN_binding_77: 6255 TATCCGATCCCG ZFN_binding_78: 6256 TGTGTGGATGACGAAACG optimal_loci_56395 OGL52 118705 ZFN_binding_79: 6257 GGAGTAAGAAATGAC ZFN_binding_80: 6258 TCCGCGTTGCTGTCTGAA optimal_loci_114664 OGL54 118711 ZFN_binding_81: 6259 TATCAGCTCGAG ZFN_binding_82: 6260 TAGACCTGTTTTGATGGTT optimal_loci_53137 OGL57 118718 ZFN_binding_83: 6261 GAAGACGGCGGCGAGAGCT ZFN_binding_84: 6262 AGGGAAGAGAGGAGGA optimal_loci_344664 OGL58 118722 ZFN_binding_85: 6263 GCACAGATCAGGGCT ZFN_binding_86: 6264 AAGGATTTGCACAGACAG optimal_loci_81941 OGL59 118726 ZFN_binding_87: 6265 GCGGCAGCCATAGGA ZFN_binding_88: 6266 GTGCATGCGTATCCA optimal_loci_321514 OGL60 118728 ZFN_binding_89: 6267 GAGGGTCTTGGGGTGATATC ZFN_binding_90: 6268 AGGAAAGCCCAAGGA optimal_loci_301180 OGL61 118732 ZFN_binding_91: 6269 GTACAAGAGTAGTAG ZFN_binding_92: 6270 TCGATCGAGGGCGCA optimal_loci_348776 OGL62 118733 ZFN_binding_93: 6271 CCACCGTCTCCGTAGGCC ZFN_binding_94: 6272 GTGTCGAGAGCT optimal_loci_244439 OGL63 118735 ZFN_binding_95: 6273 ATAGAAAACCATGGCGGAG ZFN_binding_96: 6274 AAGGGGCGGCAACGGA optimal_loci_348258 OGL64 118739 ZFN_binding_97: 6275 GTTGTCGGATAACCG ZFN_binding_98: 6276 GAGGGGGAGTAGCTAGGT optimal_loci_322501 OGL65 118742 ZFN_binding_99: 6277 GGACGAGACCAAATCG ZFN_binding_100: 6278 CAAGGAGACAAAGCT optimal_loci_244324 OGL66 118745 ZFN_binding_101: 6279 TACGTGGCAATTGGCA ZFN_binding_102: 6280 TCAGATGCTGCAGCT optimal_loci_97232 OGL67 124081 ZFN_binding_103: 6281 AGAAGATCGATCGGTA ZFN_binding_104: 6282 GCTTGAGCTCACGCA optimal_loci_282499 OGL68 125361 ZFN_binding_105: 6283 CACTACTACTACTACCGCC ZFN_binding_106: 6284 GGGTGGGGGGCA optimal_loci_155031 OGL69 118753 ZFN_binding_107: 6285 GGACCTACAATAGGCA ZFN_binding_108: 6286 GATCACAAGACCAAG optimal_loci_301773 OGL70 124878 ZFN_binding_109: 6287 CATTGTCAGTTCCTT ZFN_binding_110: 6288 CAGCAGGACTCT optimal_loci_283161 OGL71 123829 ZFN_binding_111: 6289 AAGACAGACGATGTC ZFN_binding_112: 6290 ACAAAAAAGCAAGAA optimal_loci_55524 OGL72 118761 ZFN_binding_113: 6291 TCACGGTGTTACCCATGTA ZFN_binding_114: 6292 GACGGATGCGTACGTG optimal_loci_127268 OGL73 124086 ZFN_binding_131: 6293 GTTGTTATTCAAACA ZFN_binding_132: 6294 CACAAGTAATGTGGA optimal_loci_137693 OGL74 121904 ZFN_binding_115: 6295 GCGGCTGGTTTGCAG ZFN_binding_116: 6296 CACGGACAGGAG optimal_loci_265551 OGL75 121905 ZFN_binding_117: 6297 GAGGCGGAGGTG ZFN_binding_118: 6298 AGGGCGGAAGTTACGGAG optimal_loci_128078 OGL76 121917 ZFN_binding_119: 6299 GGAGCCCCCAGCGTGGGTT ZFN_binding_120: 6300 GACCGGTCAGTAGGTCAAG optimal_loci_168286 OGL77 121918 ZFN_binding_121: 6301 TTCACGTCATGCT ZFN_binding_122: 6302 GCCGACGACTAGGAGGTA optimal_loci_3733 OGL78 121909 ZFN_binding_123: 6303 CTGTAGGGCGTCGTC ZFN_binding_124: 6304 GTAGCGGTACTACTGG optimal_loci_203075 OGL79 121912 ZFN_binding_125: 6305 ATCCAGGCAGCTGGCGGC ZFN_binding_126: 6306 GATTGGAATGCAGGCCCG optimal_loci_232484 OGL80 121981 ZFN_binding_127: 6307 GATGCGTCTGGTGTGACGAC ZFN_binding_128: 6308 ACACAGTCCTACTAG optimal_loci_136086 OGL81 124091 ZFN_binding_129: 6309 GCTCGAAAACTTATG ZFN_binding_130: 6310 ATGAAAGATGACCGA optimal_loci_228254 OGL55 n/a TTCATGGTTGTTACCACTCatnnnatG 6686 ATCCCTTTGAAGTAAAC optimal_loci_66202 OGL47 n/a TTCTACGATTACTTCtannctGCTAGT 6687 CAGATTGAA optimal_loci_120993 OGL56 n/a TGATGCAAGGTGGCGTAAAggnngg 6688 GACATAAAGAGGCAG optimal_loci_200497 OGL53 n/a GATTACCTCCACCTTttnnctAGGCCC 6689 TAATATCGAA optimal_loci_5607 OGL03 n/a ATCCCTCTATCCTTCACGaanngaAA 6690 CGATCTCGAAGGACGAT

The Zea mays representative genomic loci zinc finger designs were incorporated into zinc finger expression vectors encoding a protein having at least one finger with a CCHC structure. See, U.S. Patent Publication No. 2008/0182332. In particular, the last finger in each protein had a CCHC backbone for the recognition helix. The non-canonical zinc finger-encoding sequences were fused to the nuclease domain of the type IIS restriction enzyme FokI (amino acids 384-579 of the sequence of Wah et al., (1998) Proc. Natl. Acad. Sci. USA 95:10564-10569) via a four amino acid ZC linker and an opaque-2 nuclear localization signal derived from Zea mays to form zinc-finger nucleases (ZFNs). See, U.S. Pat. No. 7,888,121. Zinc fingers for the various functional domains were selected for in vivo use. Of the numerous ZFNs that were designed, produced and tested to bind to the putative genomic target site, the ZFNs described in Table 8 above were identified as having in vivo activity and were characterized as being capable of efficiently binding and cleaving the unique Zea mays genomic polynucleotide target sites in planta.

ZFN Construct Assembly

Plasmid vectors containing ZFN gene expression constructs, which were identified as previously described, were designed and completed using skills and techniques commonly known in the art (see, for example, Ausubel or Maniatis). Each ZFN-encoding sequence was fused to a sequence encoding an opaque-2 nuclear localization signal (Maddaloni et al., (1989) Nuc. Acids Res. 17:7532), that was positioned upstream of the zinc finger nuclease. The non-canonical zinc finger-encoding sequences were fused to the nuclease domain of the type IIS restriction enzyme FokI (amino acids 384-579 of the sequence of Wah et al. (1998) Proc. Natl. Acad. Sci. USA 95:10564-10569). Expression of the fusion proteins was driven by the strong constitutive promoter from the Zea mays Ubiquitin gene, (which includes the 5′ untranslated region (UTR) (Toki et al., (1992) Plant Physiology 100; 1503-07). The expression cassette also included the 3′ UTR (comprising the transcriptional terminator and polyadenylation site) from the Zea mays peroxidase 5 gene (Per5) gene (US Patent Publication No. 2004/0158887). The self-hydrolyzing 2A encoding the nucleotide sequence from Thosea asigna virus (Szymczak et al., (2004) Nat Biotechnol. 22:760-760) was added between the two Zinc Finger Nuclease fusion proteins that were cloned into the construct.

The plasmid vectors were assembled using the IN-FUSION™ Advantage Technology (Clontech, Mountain View, Calif.). Restriction endonucleases were obtained from New England BioLabs (Ipswich, Mass.) and T4 DNA Ligase (Invitrogen, Carlsbad, Calif.) was used for DNA ligation. Plasmid preparations were performed using NUCLEOSPIN® Plasmid Kit (Macherey-Nagel Inc., Bethlehem, Pa.) or the Plasmid Midi Kit (Qiagen) following the instructions of the suppliers. DNA fragments were isolated using QIAQUICK GEL EXTRACTION KIT™ (Qiagen) after agarose tris-acetate gel electrophoresis. Colonies of all ligation reactions were initially screened by restriction digestion of miniprep DNA. Plasmid DNA of selected clones was sequenced by a commercial sequencing vendor (Eurofins MWG Operon, Huntsville, Ala.). Sequence data were assembled and analyzed using the SEQUENCHER™ software (Gene Codes Corp., Ann Arbor, Mich.).

Plasmids were constructed and confirmed via restriction enzyme digestion and via DNA sequencing.

Zinc Finger Cloning Via Automated Workflow

A subset of Zinc Finger Nuclease vectors were cloned via an automated DNA construction pipeline. Overall, the automated pipeline resulted in vector constructions with identical ZFN architecture as described previously. Each Zinc Finger monomer, which confers the DNA binding specificity of the ZFN, were divided into 2-3 unique sequences at a KPF amino acid motif. Both the 5′ and 3′ ends of the ZFN fragments were modified with inclusion of a BsaI recognition site (GGTCTCN) and derived overhangs. Overhangs were distributed such that a 6-8 part assembly would only result in the desired full length expression clone. Modified DNA fragments were synthesized de novo (Synthetic Genomics Incorporated, La Jolla, Calif.). A single maize backbone, pDAB118791 was used in all of the maize ZFN builds. It contained the ZmUbi1 promoter and the Opaque2 NLS as well as the FokI domain and the ZmPer5 3′UTR. Cloned in between the Opaque 2 NLS and the FokI domain was a BsaI flanked SacB gene from Bacillus subtilis. When putative ligation events were plated on Sucrose containing media, the SacB cassette acts as a negative selection agent reducing or eliminating vector backbone contamination. A second part repeatedly utilized in all builds was pDAB117462. This vector contains the first monomer FokI domain, the t2A stutter sequence, and the 2^(nd) monomer Opaque2 NLS all flanked by BsaI sites.

Using these materials as the ZFN DNA parts library, a Freedom Evo 150 (TECAN, Mannedorf, Switzerland) manipulated the addition of 75-100 ng of each DNA plasmid or synthesized fragment from 2D bar coded tubes into a PCR plate (ThermoFisher, Waltham, Mass.). BsaI (NEB, Ipswich, Mass.) and T4 DNA ligase (NEB, Ipswich, Mass.) supplemented with Bovine Serum Albumin protein (NEB, Ipswich, Mass.) and T4 DNA Ligase Buffer (NEB, Ipswich, Mass.) were added to the reaction. Reactions were cylcled (25×) with incubations for 3 minutes at 37° C. and 4 minutes at 16° C. C1000 Touch Thermo Cycler (BioRad, Hercules Calif.). Ligated material was transformed and screened in Top10 cells (Life Technologies Carlsbad, Calif.) by hand or using a Qpix460 colony picker and LabChip GX (Perkin Elmer, Waltham, Mass.). Correctly digesting colonies were sequence confirmed provided to plant transformation.

Universal Donor Construct Assembly

To support rapid testing of a large number of target loci, a novel, flexible universal donor system sequence was designed and constructed. The universal donor polynucleotide sequence was compatible with high throughput vector construction methodologies and analysis. The universal donor system was composed of at least three modular domains: a variable ZFN binding domain, a non-variable analytical and user defined features domain, and a simple plasmid backbone for vector scale up. The non-variable universal donor polynucleotide sequence was common to all donors and permits design of a finite set of assays that can be used across all of the Zea mays target sites thus providing uniformity in targeting assessment and reducing analytical cycle times. The modular nature of these domains allowed for high throughput donor assembly. Additionally, the universal donor polynucleotide sequence has other unique features aimed at simplifying downstream analysis and enhancing the interpretation of results. It contains asymmetric restriction site sequence that allows the digestion of PCR products into diagnostically predicted sizes. Sequences comprising secondary structures that were expected to be problematic in PCR amplification were removed. The universal donor polynucleotide sequence is small in size (less than 3.0 Kb). Finally, the universal donor polynucleotide sequence was built upon the high copy pUC19 backbone that allows a large amount of test DNA to be bulked in a timely fashion.

As an embodiment, an example plasmid comprising a universal donor polynucleotide sequence is provided as SEQ ID NO:5418 and FIG. 7. In an additional embodiment, a universal donor polynucleotide sequence is provided as: pDAB11846, SEQ ID NO:5419, FIG. 15; pDAB117415, SEQ ID NO:5420, FIG. 16; pDAB117416, SEQ ID NO:5421, FIG. 17; pDAB117417, SEQ ID NO:5422, FIG. 18; pDAB117419, SEQ ID NO:5423, FIG. 19; pDAB117434 SEQ ID NO:5424, FIG. 20; pDAB117418, SEQ ID NO:5425, FIG. 21; pDAB117420, SEQ ID NO:5426, FIG. 22; and, pDAB117421, SEQ ID NO:5427, FIG. 23. In another embodiment, additional sequences comprising the universal donor polynucleotide sequence with functionally expressing coding sequence or nonfunctional (promoterless) expressing coding sequences can be constructed.

In another embodiment, the universal donor polynucleotide sequence is a small 2-3 Kb modular donor system delivered as a plasmid. This is a minimal donor, comprising any number of ZFN binding sites, a short 100-150 bp template region referred to as “DNA X” or “UZI Sequence” (SEQ ID NO:5428) that carries restriction sites and DNA sequences for primer design or coding sequences, and a simple plasmid backbone (FIG. 8). The entire plasmid was inserted through NHEJ following DNA double strand breaks at the appropriate ZFN binding site; the ZFN binding sites can be incorporated tandemly. This embodiment of a universal donor polynucleotide sequence was most suitable for rapid screening of target sites and ZFNs, and sequences that were difficult to amplify are minimized in the donor.

In a further embodiment the universal donor polynucleotide sequence was made up of at least 4 modules and carries ZFN binding sites, homology arms, DNA X with either just the approximately 100 bp analytical piece or coding sequences. This embodiment of the universal donor polynucleotide sequence was suitable for interrogating HDR mediated gene insertion at a variety of target sites, with several ZFNs (FIG. 9).

The universal donor polynucleotide sequence can be used with all targeting molecules with defined DNA binding domains, with two modes of targeted donor insertion (NHEJ/HDR). As such, when the universal donor polynucleotide sequence was co-delivered with the appropriate ZFN expression construct, the donor vector and the maize genome was cut in one specific location dictated by the binding of the particular ZFN. Once linearized, the donor can be incorporated into the genome by NHEJ or HDR. The different analytical considerations in the vector design can then be exploited to determine the Zinc Finger which maximizes the efficient delivery of targeted integration. (FIG. 10).

Example 4: Zea mays Transformation Procedures

Before delivery to Zea mays c.v. Hi-II protoplasts, plasmid DNA for each ZFN construct was prepared from cultures of E. coli using the PURE YIELD PLASMID MAXIPREP SYSTEM® (Promega Corporation, Madison, Wis.) or PLASMID MAXI KIT® (Qiagen, Valencia, Calif.) following the instructions of the suppliers.

Protoplast Isolation

Zea mays c.v. Hi-II suspension cells were maintained at a 3.5 day maintenance schedule, 4 mL packed cell volume (PCV) of cells were collected and transferred to 50 mL sterile conical tubes (Fisher Scientific) containing 20 mL of enzyme solution (0.6% PECTOLYASE™, 6% CELLULASE™ (“Onozuka” R10; Yakult Pharmaceuticals, Japan), 4 mM MES (pH 5.7), 0.6 M mannitol, 15 mM MgCl₂). The cultures were capped and wrapped in PARAFILM™ and placed on a platform rocker (Thermo Scientific, Vari Mix platform Rocker) at speed setting 10 for incubation for 16-18 hours at room temperature until protoplasts were released. Following incubation, a drop of cells was checked under microscope to check the quality of digestion and digested cells were filtered through 100 μm cell strainer, rinsed with 10 mL W5 media [2 mM MES (pH5.7), 205 mM NaCl, 167 mM CaCl₂, 6.7 mM KCl], followed by filtering through 70 μm and 40 μm cell strainers. The 100 μm and 40 μm strainer was rinsed with 10 mL W5 media. The filtered protoplasts along with rinsed media were collected in 50 mL centrifuge tube and final volume was approximately 40 mL. 8 mL of “Heavy Gradient solution” [500 mM sucrose, 1 mM CaCl₂, 5 mM MES (pH6.0)] was then slowly added to the bottom of the protoplast/enzyme solution, centrifuged in a centrifuge with a swing arm bucket rotor for 15 minutes at 300-350×g. Following centrifugation, about 7-8 mL of protoplast band was removed, washed with 25 mL of W5, and centrifuged for 15 minutes at 180-200×g. The protoplasts were then resuspended in 10 mLs of MMG solution [4 mM MES (pH 5.7), 0.6 M mannitol, 15 mM MgCl₂]. Protoplasts were counted using a haemocytometer or flow cytometer and diluted to 1.67 million per mL using MMG.

Transformation of Zea mays c.v. HI-II Suspension Culture Derived Protoplasts Using PEG

Approximately 0.5 million protoplasts (300 μl in MMG solution) were transferred to 2 mL tubes, and mixed with 40 μl of DNA and incubated at room temperature for 5-10 minutes. Next, 300 μl of freshly prepared PEG solution [36% PEG 4000, 0.3 M mannitol, 0.4M CaCl₂] was added, and the mixture was incubate at room temperature 15-20 minutes with periodic mixing by inversion. After incubation, 1 ml of W5 wash was added slowly and mixed gently and protoplasts were pelleted by centrifugation at 180-200×g for 15 minutes. The pellet was resuspended in 1 mL of WI media [4 mM MES (pH 5.7), 0.6 M mannitol, 20 mM KCl] and protoplast containing tube wrapped with aluminum foil and incubated in room temperature overnight for about 16 hours.

Transformation of ZFN and Donor

For each of the selected genomic loci of Table 5, the Zea mays protoplasts were transfected with a yfp gene expressing control, ZFN alone, donor alone and a mixture of ZFN and donor at 1:10 ratio (by weight). The total amount of DNA for transfection of 0.5 million protoplasts was 80 μg. All treatments were conducted in replicates of either 3 or 6. The yfp gene expressing control used was pDAB8393 (FIG. 11) containing the Zea mays Ubiquitin 1 promoter—yellow fluorescent protein coding sequence—Zea mays Per5 3′UTR and the Rice Actin1 promoter—pat coding sequence—Zea mays lipase 3′UTR gene expression cassettes. To provide a consistent amount of total DNA per transfection, either salmon sperm or a plasmid containing the yfp gene was used as filler where necessary. In a typical targeting experiment, 4 μg of ZFN alone or with 36 μg of donor were transfected and appropriate amount of salmon sperm or pUC19 plasmid DNA was added to bring the overall amount of DNA to 80 μg. Inclusion of yfp gene expressing plasmid as filler allows assessment of transfection quality across multiple loci and replicate treatments.

Example 5: Cleavage of Genomic Loci in Zea mays Via Zinc Finger Nuclease

ZFN transfected Zea mays c.v. Hi-II protoplasts were harvested 24 hours post-transfection, by centrifugation at 1600 rpm in 2 ml EPPENDORF™ tubes and the supernatant was completely removed. Genomic DNA was extracted from protoplast pellets using the QIAGEN PLANT DNA EXTRACTION KIT™ (Qiagen, Valencia, Calif.). The isolated DNA was resuspended in 50 μL of water and concentration was determined by NANODROP® (Invitrogen, Grand Island, N.Y.). The integrity of the DNA was estimated by running samples on 0.8% agarose gel electrophoresis. All samples were normalized (20-25 ng/μL) for PCR amplification to generate amplicons for sequencing (Illumina, Inc., SanDiego, Calif.). Bar-coded PCR primers for amplifying regions encompassing each test ZFN recognition sequence from treated and control samples were designed and purchased from IDT (Coralville, Iowa, HPLC purified). Optimum amplification conditions were identified by gradient PCR using 0.2 μM appropriate bar-coded primers, ACCUPRIME PFX SUPERMIX™ (Invitrogen, Carlsbad, Calif.) and 100 ng of template genomic DNA in a 23.5 μL reaction. Cycling parameters were initial denaturation at 95° C. (5 min) followed by 35 cycles of denaturation (95° C., 15 sec), annealing (55-72° C., 30 sec), extension (68° C., 1 min) and a final extension (68° C., 7 min). Amplification products were analyzed on 3.5% TAE agarose gels and appropriate annealing temperature for each primer combination was determined and used to amplify amplicons from control and ZFN treated samples as described above. All amplicons were purified on 3.5% agarose gels, eluted in water and concentrations were determined by NANODROP™. For Next Generation Sequencing, approximately 100 ng of PCR amplicon from the ZFN treated and corresponding maize protoplast controls were pooled together and sequenced using llumina Next Generation Sequencing (NGS).

The cleavage activity of appropriate ZFNs at each Zea mays selected genomic loci were assayed. Short amplicons encompassing the ZFN cleavage sites were amplified from the genomic DNA and subjected to Illumina NGS from ZFN treated and control protoplasts. The ZFN induced cleavage or DNA double strand break was resolved by the cellular NHEJ repair pathway by insertion or deletion of nucleotides (indels) at the cleavage site and presence of indels at the cleavage site is thus a measure of ZFN activity and is determined by NGS. Cleavage activity of the target specific ZFNs was estimated as the number of sequences with indels per 1 million high quality sequences using NGS analysis software (Patent publication 2012-0173,153, data Analysis of DNA sequences) (FIG. 12). Activities in the range of 5-100 fold over controls were observed for Zea mays selected genomic loci targets and were further confirmed by sequence alignments that showed a diverse footprint of indels at each ZFN cleavage site. This data suggests that the Zea mays selected genomic loci were amenable to cleavage by ZFNs. Differential activity at each target was reflective of its chromatin state and amenability to cleavage as well as the efficiency of expression of each ZFN.

Example 6: Rapid Targeting Analysis of the Integration of a Polynucleotide Donor

Validation of the targeting of the universal donor polynucleotide sequence within the Zea mays selected genomic loci targets via non-homologous end joining (NHEJ) meditated donor insertion, was performed using a semi-throughput protoplast based Rapid Testing Analysis method. For each Zea mays selected genomic loci target, 3-6 ZFN designs were tested and targeting was assessed by measuring ZFN mediated cleavage by Next Generation Sequencing methods (FIG. 12) and donor insertion by junctional in-out PCR (FIG. 13). Zea mays selected genomic loci that were positive in both assays were identified as a targetable locus.

ZFN Donor Insertion Rapid Testing Analysis

To determine if a Zea mays selected genomic loci target can be targeted for donor insertion, a ZFN construct and universal donor polynucleotide construct were co-delivered to maize protoplasts which were incubated for 24 hours before the genomic DNA was extracted for analysis. If the expressed ZFN was able to cut the target binding site both at the Zea mays selected genomic loci target and in the donor, the linearized donor would then be inserted into the cleaved target site in the maize genome via the non-homologous end joining (NHEJ) pathway. Confirmation of targeted integration at the Zea mays selected genomic loci target was completed based on an “In-Out” PCR strategy, where an “In” primer recognizes sequence at the native optimal genomic loci and an “Out” primer binds to sequence within the donor DNA. The primers were designed in a way that only when the donor DNA was inserted at the Zea mays selected genomic loci target, would the PCR assay produce an amplification product with the expected size. The In-Out PCR assay was performed at both the 5′- and 3′-ends of the insertion junction. The primers used for the analysis of integrated polynucleotide donor sequences are provided in Table 9.

ZFN Donor Insertion at Target Loci Using Nested “in-Out” PCR

All PCR amplifications were conducted using a TAKARA EX TAQ HS™ kit (Clonetech, Mountain View, Calif.). The first In-Out PCR was carried out in 20 μL final reaction volume that contains 1× TAKARA EX TAQ HS™ buffer, 0.2 mM dNTPs, 0.2 μM “Out” primer (Table 9), 0.05 μM “In” primer (designed from the universal donor cassette described above), 0.75 unit of TAKARA EX TAQ HS™ polymerase, and 10 ng extracted maize protoplast DNA. The reaction was then carried out using a PCR program that consisted of 94° C. for 2 min, 20 cycles of 98° C. for 12 sec and 68° C. for 2 min, followed by 72° C. for 10 min and held at 4° C. Final PCR products were run on an agarose gel along with 1 KB PLUS DNA LADDER™ (Life Technologies, Grand Island, N.Y.) for visualization.

The nested In-Out PCR was conducted in 20 μL final reaction volume that contained 1× TAKARA EX TAQ HS™ buffer, 0.2 mM dNTPs, 0.2 μM “Out” primer (Table 9), 0.1 μM “In” primer (designed from the universal donor cassette described above, Table 10), 0.75 unit of TAKARA EX TAQ HS™ polymerase, and 1 μL of the first PCR product. The reaction was then carried out using a PCR program that consisted of 94° C. for 2 min, 31 cycles of 98° C. for 12 sec, 66° C. for 30 sec and 68° C. for 45 sec, followed by 72° C. for 10 min and held at 4° C. Final PCR products were run on an agarose gel along with 1 KB PLUS DNA LADDER™ (Life Technologies, Grand Island, N.Y.) for visualization.

TABLE 9 List of all “Out” primers for nested In-Out PCR analysis of optimal genomic loci. OGL1 First 5′- APL02- SEQ ID NO: 5430 PCR end 5PriF1 CGCCACAAATCTGAACCAGCA Spec- SEQ ID NO: 5431 PriR1 CCACGATCGACATTGATCTGGCTA 3′- APL02- SEQ ID NO: 5432 end 3PriR1 GCGACATATCAGGCCAACAGG Uzi- SEQ ID NO: 5433 PriF1 GGGATATGTGTCCTACCGTATCAGG Nest 5′- APL02- SEQ ID NO: 5434 PCR end 5nstPriF1 CCAGCATACAGTTAGGGCCCA Spec- SEQ ID NO: 5435 nstPriR1 GTTGCCTTGGTAGGTCCAGC 3′- APL02- SEQ ID NO: 5436 end 3nstPriR1 CGAAAACTCAGCATGCGGGAA Uzi- SEQ ID NO: 5437 nstPriF1 GAGCCATCAGTCCAACACTGC OGL2 First 5′- APL01- SEQ ID NO: 5438 PCR end 5PriF1 ACAGGCGTACAGCAACACCA 3′- APL01- SEQ ID NO: 5439 end 3PriR1 GACCCTATGGTGTTGGATCCCA Nest 5′- APL01- SEQ ID NO: 5440 PCR end 5nstPriF1 CGGGAGCTAGGCAACAAATCG 3′- APL01- SEQ ID NO: 5441 end 3nstPriR1 TCTGACTAAACGGGTGGATGCTG OGL8 First 5′- OGL08- SEQ ID NO: 5442 PCR end 5nstPriF2 CGGATCAGTTGATTCGCTCACTTTCA 3′- OGL08- SEQ ID NO: 5443 end 3priR GCCGAAAAGCAGCAACTGGAA Nest 5′- OGL08- SEQ ID NO: 6619 PCR end 5nstPriF GATTGCTACGCAGACCGCCTA 3′- OGL08- SEQ ID NO: 5444 end 3nstPriR CACTATTCCTCCGGCATGCAG OGL11 First 5′- OGL11- SEQ ID NO: 5445 PCR end 5PriF TGACCTATTGATCGGTCGGCTC 3′- OGL11- SEQ ID NO: 5446 end 3PriR2 TGCCTTGAATCTCAGGGATGCA Nest 5′- OGL11- SEQ ID NO: 5447 PCR end 5nstPriF GCCGAAGCTAACTAGCGGACA 3′- OGL11- SEQ ID NO: 5448 end 3nstPriR2 CATGGAGTAGCAGCTGTGCTG OGL12 First 5′- OGL12- SEQ ID NO: 5449 PCR end 5PriF GAAAAGCAGTCACCGGCTCTG 3′- OGL12- SEQ ID NO: 5450 end 3PriR CCATGGACATGAATTCGGCACG Nest 5′- OGL12- SEQ ID NO: 5451 PCR end 5nstPriF CTTTTGCACCACGGAGCAGAC 3′- OGL12- SEQ ID NO: 5452 end 3nstPriR GCTAGCAAAACTTTGAAGCTCGCTC OGL13 First 5′- OGL13 SEQ ID NO: 5453 PCR end 5PriF GAGGTCCCTTACGGGTCATCG 3′- OGL13- SEQ ID NO: 5454 end 3PriR ACCAGGTCTATCTTGCGCAGAC Nest 5′- OGL13- SEQ ID NO: 5455 PCR end 5nstPriF AATAGCGTGGTCGGGTCCTAG 3′- OGL13- SEQ ID NO: 5456 end 3nstPriR ACGAACGATCCAAGGTGCAGT OGL14 First 5′- OGL14- SEQ ID NO: 5457 PCR end 5PriF TAGAGACGAGGACTCTGGGCT 3′- OGL14- SEQ ID NO: 5458 end 3PriR AAGTCCAACATGGGCACAACC Nest 5′- OGL14- SEQ ID NO: 5459 PCR end 5nstPriF CCTCGTTAAGGGTGCAGGTTG 3′- OGL14- SEQ ID NO: 5460 end 3nstPriR CCAAGTCAGCTTCTAAGCCATCAAAC OGL15 First 5′- OGL15- SEQ ID NO: 5461 PCR end 5PriF AACCCTAGACTTCTGCCTGGTG 3′- OGL15- SEQ ID NO: 5462 end 3PriR GCTCACTTACGAGCAGATCCCA Nest 5′- OGL15- SEQ ID NO: 5463 PCR end 5nstPriF GGTGCACGCATGTTCTCATGT 3′- OGL15- SEQ ID NO: 5464 end 3nstPriR TGTTTACCGCAGCCATGCTTG OGL16 First 5′- OGL16- SEQ ID NO: 5465 PCR end 5PriF GTTGTATACGGCATCCATCCGCT 3′- OGL16- SEQ ID NO: 5466 end 3PriR GAATGAAACTGGTGGTCTGCTCC Nest 5′- OGL16- SEQ ID NO: 5467 PCR end 5nstPriF CCGACGAGGTACAAGTAGCAGG 3′- OGL16- SEQ ID NO: 5468 end 3nstPriR CCCGTAGTCCAGATTCTTGTGGT OGL17 First 5′- OGL17- SEQ ID NO: 5469 PCR end 5PriF GTCGTTTGTTCGGAAGGGGAG 3′- OGL17- SEQ ID NO: 5470 end 3PriR CGTAGTTGTCCGGCATGTCCT Nest 5′- OGL17- SEQ ID NO: 5471 PCR end 5nstPriF TGTATCCCTTCGGTGAGCACG 3′- OGL17- SEQ ID NO: 5472 end 3nstPriR TGAATCGACTCGCTGACAGGTG OGL04 First 5′- OGL04- SEQ ID NO: 6311 PCR end 5PriF CAACCAGAAACGTCCTGCACTG Spec- SEQ ID NO: 6312 PriR1 CCACGATCGACATTGATCTGGCTA 3′- OGL04- SEQ ID NO: 6313 end 3PriR AAATCCAAGCCACGTACGCAC UnivDonor- SEQ ID NO: 6314 3PriF1 GTTTCATCAAGCCTTACGGTCACC Nest 5′- OGL04- SEQ ID NO: 6315 PCR end 5nstPriF ACACCAATTGCCCATTTGGCA Spec- SEQ ID NO: 6316 nstPriR2 GCTGGCGATGAGCGAAATGTAG 3′- OGL04- SEQ ID NO: 6317 end 3nstPriR TTGGTTAGCAGCACGGATGGA UnivDonor- SEQ ID NO: 6318 3PriF2 CAGCAACGTCGGTTCGAGATG OGL05 First 5′- OGL05-1- SEQ ID NO: 6319 PCR end 5PriF ATGCCACTTTCGAAGAGAGGACG 3′- OGL05-1- SEQ ID NO: 6320 end 3PriR2 CATCTCCAACGTCATCGGCAC Nest 5′- OGL05-1- SEQ ID NO: 6321 PCR end 5nstPriF GGGAAACAGATTCGTCAGCTTGC 3′- OGL05-1- SEQ ID NO: 6322 end 3nstPriR GCCTATCCAGTGGCGGATACA OGL06 First 5′- OGL06- SEQ ID NO: 6323 PCR end 5PriF CTTGCTCTACAACTCTGCCCCA Spec- SEQ ID NO: 6324 PriR1 CCACGATCGACATTGATCTGGCTA 3′- OGL06- SEQ ID NO: 6325 end 3PriR AGTCGGTACCTGCAAGCTACG UnivDonor- SEQ ID NO: 6326 3PriF1 GTTTCATCAAGCCTTACGGTCACC Nest 5′- OGL06- SEQ ID NO: 6327 PCR end 5nstPriF TGGATTTGAGGCCAACTGCAC Spec- SEQ ID NO: 6328 nstPriR2 GCTGGCGATGAGCGAAATGTAG 3′- OGL06- SEQ ID NO: 6329 end 3nstPriR TCTGCATTGTTGGGATCGACCA UnivDonor- SEQ ID NO: 6330 3PriF2 CAGCAACGTCGGTTCGAGATG OGL07 First 5′- OGL07-1- SEQ ID NO: 6331 PCR end 5nstPriF ACGATCGCAGGTTATCCTCGC 3′- OGL07-1- SEQ ID NO: 6332 end 3PriR CTTGTCGGTTGCTGTGTGGAC Nest 5′- OGL07-1- SEQ ID NO: 6333 PCR end 5nstPriF AACACGGATGGCCTGCAATG 3′- OGL07-1- SEQ ID NO: 6334 end 3nstPriR GCATGGGCGTACGTCACTTG OGL09 First 5′- OGL09- SEQ ID NO: 6335 PCR end 5PriF ACCCAGAATCTCTGGTTCCGT 3′- OGL09- SEQ ID NO: 6336 end 3PriR CAGGAAGCTCTGCATCTGCG Nest 5′- OGL09- SEQ ID NO: 6337 PCR end 5nstPriF AGTCTTTGATGTAAACGTCTTGCCT 3′- OGL09- SEQ ID NO: 6338 end 3nstPriR GCATGGAAACACCAGGTCGA OGL10 First 5′- OGL10- SEQ ID NO: 6339 PCR end 5PriF GCAGCGAATAGGAATGCGAGAC 3′- OGL10- SEQ ID NO: 6340 end 3PriR TAACCTTGTTTCGCTGACTCCC Nest 5′- OGL10- SEQ ID NO: 6341 PCR end 5nstPriF CTTCTTCTACCTACACGCACCAG 3′- OGL10- SEQ ID NO: 6342 end 3nstPriR GATCCGTTTCCTCACTCTCGC OGL18 First 5′- OGL18- SEQ ID NO: 6343 PCR end 5PriF AGGTGAATCTTCCGTGGCTGT 3′- OGL18- SEQ ID NO: 6344 end 3PriR CCATAATCAGTGTGACTGGTGGCT Nest 5′- OGL18- SEQ ID NO: 6345 PCR end 5nstPriF CGGATCTAAGGTGCCCTGTCT 3′- OGL18- SEQ ID NO: 6346 end 3nstPriR GTCTAGCTCATGGAAGTGGGAGG OGL19 First 5′- OGL19- SEQ ID NO: 6347 PCR end 5PriF GACTTCTAAGCCCCAAGGCCTA 3′- OGL19- SEQ ID NO: 6348 end 3PriR2 AGATCTTTTGGCTCCCTCTCACC Nest 5′- OGL19- SEQ ID NO: 6349 PCR end 5nstPriF GTGCTTCGAGGGCTCAAGGTA 3′- OGL19- SEQ ID NO: 6350 end 3nstPriR2 ATTGCTCACCCCATCCCCTT OGL20 First 5′- OGL20- SEQ ID NO: 6351 PCR end 5PriF GGCTATGACCCGGACACTACC 3′- OGL20- SEQ ID NO: 6352 end 3PriR CAGTTGGGCGTCAAGTTAGTTCAG Nest 5′- OGL20- SEQ ID NO: 6353 PCR end 5nstPriF AAGTCCACAAGGATCTGACCACG 3′- OGL20- SEQ ID NO: 6354 end 3nstPriR TGAAACTTTGGTTCAGTCTGCTCG OGL21 First 5′- OGL21- SEQ ID NO: 6355 PCR end 5PriF TATGTCCAAGCCACGAGAAGC 3′- OGL21- SEQ ID NO: 6356 end 3PriR ACTGCAGGTACTACTGGTACGC Nest 5′- OGL21- SEQ ID NO: 6357 PCR end 5nstPriF GCTACAGTATAGCAGGAGCAGC 3′- OGL21- SEQ ID NO: 6358 end 3nstPriR GTCCTACTATACGCTGCCGC OGL22 First 5′- OGL22- SEQ ID NO: 6359 PCR end 5PriF CAATCCTTCTGAGCTGCACCG 3′- OGL22- SEQ ID NO: 6360 end 3PriR GGTGTCAATGACCTCACGAGC Nest 5′- OGL22- SEQ ID NO: 6361 PCR end 5nstPriF CCGTACCAAACAGGCAAGCAG 3′- OGL22- SEQ ID NO: 6362 end 3nstPriR GATCGCCCATATGCTTGGATTCAC OGL23 First 5′- OGL23- SEQ ID NO: 6363 PCR end 5PriF GGATTAGGACGGCTGACTGGT 3′- OGL23- SEQ ID NO: 6364  end 3PriR GTTGCTTTGTTTGCGTGCTCC Nest 5′- OGL23- SEQ ID NO: 6365 PCR end 5nstPriF TTAAAGTGCTAGCTGACTGACCGA 3′- OGL23- SEQ ID NO: 6366 end 3nstPriR GGCCCATGCCTTAGGTTGAC OGL24 First 5′- OGL24- SEQ ID NO: 6367 PCR end 5PriF ACTGAGACTGGGAGTCTGGGA 3′- OGL24- SEQ ID NO: 6368 end 3PriR CGCCGTCCGACTGTTATTACC Nest 5′- OGL24- SEQ ID NO: 6369 PCR end 5nstPriF CTTCGGCCTTGGATTGGATCAC 3′- OGL24- SEQ ID NO: 6370 end 3nstPriR ACAACGCAGATCCCTAGAATCCA OGL25 First 5′- OGL25- SEQ ID NO: 6371 PCR end 5PriF GGGATCTCTTGTCACCAAATCAGC 3′- OGL25- SEQ ID NO: 6372 end 3PriR TTGACAGTGAGACATGGGAGTACC Nest 5′- OGL25- SEQ ID NO: 6373 PCR end 5nstPriF TGCCTGCATTGCATCGATCTG 3′- OGL25- SEQ ID NO: 6374 end 3nstPriR AGTACCCACTGTCACTGCACG OGL26 First 5′- OGL26- SEQ ID NO: 6375 PCR end 5PriF ATCTTCACCAAGTATCCCACACCT 3′- OGL26- SEQ ID NO: 6376 end 3PriR2 GCTGTGTTAGTATCGTCGAAGGCT Nest 5′- OGL26- SEQ ID NO: 6377 PCR end 5nstPriF TCAAACCTCACCTGATGTATCGCT 3′- OGL26- SEQ ID NO: 6378 end 3nstPriR2 CGAACCTCCAATTTATCGGCAATCG OGL27 First 5′- OGL27- SEQ ID NO: 6379 PCR end 5PriF AAGTCCCTAGAGCCCTCATGC 3′- OGL27- SEQ ID NO: 6380 end 3PriR GAGAGTTAGGAGGGAGCATGGC Nest 5′- OGL27- SEQ ID NO: 6381 PCR end 5nstPriF GTGTCCGAGATAGGTCGTGTCC 3′- OGL27- SEQ ID NO: 6382 end 3nstPriR TTGAACTTGGGCATGAGTGGGA OGL28 First 5′- OGL28- SEQ ID NO: 6383 PCR end 5PriF GTCGGCTGTGCGTTATGAGAC 3′- OGL28- SEQ ID NO: 6384 end 3PriR GATTAATCGGTTATCGGTGGACGC Nest 5′- OGL28- SEQ ID NO: 6385 PCR end 5nstPriF ACGGACAGATCACAGATCGGG 3′- OGL28- SEQ ID NO: 6386 end 3nstPriR CCTTAATCCGGTTTGGTGAACCC OGL29 First 5′- OGL29- SEQ ID NO: 6387 PCR end 5PriF GCTTACACCGATGCAGGGGTA 3′- OGL29- SEQ ID NO: 6388 end 3PriR GGTTGACATCGGAATTCGTGCC Nest 5′- OGL29- SEQ ID NO: 6389 PCR end 5nstPriF TGAAAGAGAGCGGCCCAACTAC 3′- OGL29- SEQ ID NO: 6390 end 3nstPriR TTAATGCTGGCCTCTCCTGCA OGL30 First 5′- OGL30- SEQ ID NO: 6391 PCR end 5PriF ATGAAGAGCACCAGCTACCCC 3′- OGL30- SEQ ID NO: 6392 end 3PriR GGAAGATGGAACCACATGCCC Nest 5′- OGL30- SEQ ID NO: 6393 PCR end 5nstPriF GGCTACAAAACCCAAGAGGGG 3′- OGL30- SEQ ID NO: 6394 end 3nstPriR CCCTTTCATGCAACGATCAGGC OGL31 First 5′- OGL31- SEQ ID NO: 6395 PCR end 5PriF TGTTCAGTTGGTAAGTCGTCGCT 3′- OGL31- SEQ ID NO: 6396 end 3PriR GTTCTTGGAGAGTGATTGTCGGC Nest 5′- OGL31- SEQ ID NO: 6397 PCR end 5nstPriF CTTCACCTCAAGGGAAGCAAGC 3′- OGL31- SEQ ID NO: 6398 end 3nstPriR GGTGAAACTGAGCTGGGAATTGG OGL32 First 5′- OGL32- SEQ ID NO: 6399 PCR end 5PriF GATCCACAACCACATTCAACAAGGT 3′- OGL32- SEQ ID NO: 6400 end 3PriR TGATCAAACTAGAGGCCTGATGACG Nest 5′- OGL32- SEQ ID NO: 6401 PCR end 5nstPriF GGACAAATGACATGTAACCCACTCC 3′- OGL32- SEQ ID NO: 6402 end 3nstPriR ATGACGACAGCGTGTTTGTGG OGL33 First 5′- OGL33- SEQ ID NO: 6403 PCR end 5PriF AGCTCCACTTCCAGTAGTCCTG 3′- OGL33- SEQ ID NO: 6404 end 3PriR CGGATAGCGTCCACAAACGAG Nest 5′- OGL33- SEQ ID NO: 6405 PCR end 5nstPriF AATCATGCGGCTGTCGAAAGG 3′- OGL33- SEQ ID NO: 6406 end 3nstPriR GCGATAAGAAAGCATCCTGCGG OGL34 First 5′- OGL34- SEQ ID NO: 6407 PCR end 5PriF ACTGTACCACCGAAAGACGACC 3′- OGL34- SEQ ID NO: 6408 end 3PriR CCCGTCTCACTGTGGATCTATGTC Nest 5′- OGL34- SEQ ID NO: 6409 PCR end 5nstPriF AAAGACGACCAAACAGTCCTGC 3′- OGL34- SEQ ID NO: 6410 end 3nstPriR GAGTCAACGTGTCAGTGTCACC OGL35 First 5′- OGL35- SEQ ID NO: 6411 PCR end 5PriF AGGTGTAGTCCTGCTCTGTCTG 3′- OGL35- SEQ ID NO: 6412 end 3PriR AACTGAAGACACTGACGACATCCA Nest 5′- OGL35- SEQ ID NO: 6413 PCR end 5nstPriF TAGGGCGCTAGGCATGTACTC 3′- OGL35- SEQ ID NO: 6414 end 3nstPriR GTGGCCTTCTAGGTACACTAGGG OGL36 First 5′- OGL36- SEQ ID NO: 6415 PCR end 5PriF GCAACCAACTTTGTCGGATGCT 3′- OGL36- SEQ ID NO: 6416 end 3PriR AAAGCTCACCTCACAGCACGA Nest 5′- OGL36- SEQ ID NO: 6417 PCR end 5nstPriF TCATAGATTTCGCGTGGTTGAACTG 3′- OGL36- SEQ ID NO: 6418 end 3nstPriR ACTCTGCAGCCATGAATTCCAC OGL37 First 5′- OGL37- SEQ ID NO: 6419 PCR end 5PriF GAGAAACCGAGGGATCGGAACA 3′- OGL37- SEQ ID NO: 6420 end 3PriR ACATGTACGTGTGCGAGAGTCG Nest 5′- OGL37- SEQ ID NO: 6421 PCR end 5nstPriF AGTACGACTGGAATCCAACGCG 3′- OGL37- SEQ ID NO: 6422 end 3nstPriR CTCTCCCTAGCTCGACGCTTG OGL38 First 5′- OGL38- SEQ ID NO: 6423 PCR end 5PriF GTAGCACTGCACCGTTCATGC 3′- OGL38- SEQ ID NO: 6424 end 3PriR ACTCTCCTTCCCTCGACGGTA Nest 5′- OGL38- SEQ ID NO: 6425 PCR end 5nstPriF AGGAGATGAAGGCTTTGTCCCC 3′- OGL38- SEQ ID NO: 6426 end 3nstPriR GCAAACCTGCATGGTTGATGC OGL39 First 5′- OGL39- SEQ ID NO: 6427 PCR end 5PriF TTGGGTTTGTGCACCACACTC 3′- OGL39- SEQ ID NO: 6428 end 3PriR GCTTCTGGAAAAACGCCAGCA Nest 5′- OGL39- SEQ ID NO: 6429 PCR end 5nstPriF ATTCCTTGCGCTCCGTACGAA 3′- OGL39- SEQ ID NO: 6430 end 3nstPriR CTTTGCATTGCAGGCACGGTTA OGL40 First 5′- OGL40- SEQ ID NO: 6431 PCR end 5PriF CCGAGGTTAAATCCACAGGCG 3′- OGL40- SEQ ID NO: 6432 end 3PriR GCGCATTTCCTTGCCCTCAAA Nest 5′- OGL40- SEQ ID NO: 6433 PCR end 5nstPriF GTTCACAGGTACGACAGCAGC 3′- OGL40- SEQ ID NO: 6434 end 3nstPriR TACGTTGCCACCAAAAGAGCC OGL41 First 5′- OGL41- SEQ ID NO: 6435 PCR end 5PriF AGCAGGCTACTGTGGTCAGG 3′- OGL41- SEQ ID NO: 6436 end 3PriR CGATTGCATACAGCAGGTGCC Nest 5′- OGL41- SEQ ID NO: 6437 PCR end 5nstPriF GGCAGGTTTTGAAGGACCCC 3′- OGL41- SEQ ID NO: 6438 end 3nstPriR ACGAGCAATGCAGTGAAGGGT OGL42 First 5′- OGL42- SEQ ID NO: 6439 PCR end 5PriF TGAGAACGAAACCCGTCAAGCA 3′- OGL42- SEQ ID NO: 6440 end 3PriR CACGTCGATCAAACGGCGAG Nest 5′- OGL42- SEQ ID NO: 6441 PCR end 5nstPriF CGTCAAGCATGCAGAAAGGCT 3′- OGL42- SEQ ID NO: 6442 end 3nstPriR CCCCTAATCCGCACCGTGTA OGL43 First 5′- OGL43- SEQ ID NO: 6443 PCR end 5PriF CCTGTTCCTTCTCCCGAATGC 3′- OGL43- SEQ ID NO: 6444 end 3PriR GGTACAAAGTGAAAAGGGCCGG Nest 5′- OGL43- SEQ ID NO: 6445 PCR end 5nstPriF GTGCAATCAAGCCTTGCCCAT 3′- OGL43- SEQ ID NO: 6446 end 3nstPriR GAAGTGATGGTCCCTGCCAC OGL44 First 5′- OGL44- SEQ ID NO: 6447 PCR end 5PriF GGCTCTAACACATGGTGAGGC 3′- OGL44- SEQ ID NO: 6448 end 3PriR AATCATGGTCCTAGTTGTAGCCCC Nest 5′- OGL44- SEQ ID NO: 6449 PCR end 5nstPriF ACTAGGATGAGGGAGCCAATGG 3′- OGL44- SEQ ID NO: 6450 end 3nstPriR CTATGGAGATGCCTCCCACCAT OGL45 First 5′- OGL45- SEQ ID NO: 6451 PCR end 5PriF GAAGAGCTCGGCATCGGAGAT 3′- OGL45- SEQ ID NO: 6452 end 3PriR TCCCAAAACGAACTGTGTGCG Nest 5′- OGL45- SEQ ID NO: 6453 PCR end 5nstPriF TGGCTAGAGCGACCTTGTTCG 3′- OGL45- SEQ ID NO: 6454 end 3nstPriR TCGAGATCAGGCATCCACACC OGL46 First 5′- OGL46- SEQ ID NO: 6455 PCR end 5PriF CCAAAGTATTTGGTGGGATTCTCGC 3′- OGL46- SEQ ID NO: 6456 end 3PriR CTGCAACAAGTGAAAAGCGCC Nest 5′- OGL46- SEQ ID NO: 6457 PCR end 5nstPriF GGATTCTCGCTTTTTCCCACCAAG 3′- OGL46- SEQ ID NO: 6458 end 3nstPriR TACATCGATCCAGCTCGTGCTG OGL47 First 5′- OGL47- SEQ ID NO: 6459 PCR end 5PriF CGGAACACTAAAACGGGGACATG Spec- SEQ ID NO: 6460 PriR1 CCACGATCGACATTGATCTGGCTA 3′- OGL47- SEQ ID NO: 6461 end 3PriR TCTTCCTGGCAAGCACTAGGAAC UnivDonor- SEQ ID NO: 6462 3PriF1 GTTTCATCAAGCCTTACGGTCACC Nest 5′- OGL47- SEQ ID NO: 6463 PCR end 5nstPriF ACCGAGTAAGGGCTTGTTCGG Spec- SEQ ID NO: 6464 nstPriR2 GCTGGCGATGAGCGAAATGTAG 3′- OGL47- SEQ ID NO: 6465 end 3nstPriR TCTCCAGCAACCCCTAGATGC UnivDonor- SEQ ID NO: 6466 3PriF2 CAGCAACGTCGGTTCGAGATG OGL48 First 5′- OGL48- SEQ ID NO: 6467 PCR end 5PriF GCAGTGACACTATAGCCACGTGT 3′- OGL48- SEQ ID NO: 6468 end 3PriR GCCCAATCAATTGTCCCTGGAC Nest 5′- OGL48- SEQ ID NO: 6469 PCR end 5nstPriF TGCTACCCAATGGTGTGGACTT 3′- OGL48- SEQ ID NO: 6470 end 3nstPriR AATGCCCATTCGGTTGAACCC OGL49 First 5′- OGL49- SEQ ID NO: 6471 PCR end 5PriF TCTGATGATCGGGTTGAGGCC 3′- OGL49- SEQ ID NO: 6472 end 3PriR CCTCCGGAATCATTTCCCGTTG Nest 5′- OGL49- SEQ ID NO: 6473 PCR end 5nstPriF GTGCTGATCTGGTTGTGGGTC 3′- OGL49- SEQ ID NO: 6474 end 3nstPriR CGGAACAATTCCTGGGCACAA OGL50 First 5′- OGL50- SEQ ID NO: 6475 PCR end 5PriF AGCTATGGTTAACGGGAATGCCA Spec- SEQ ID NO: 6476 PriR1 CCACGATCGACATTGATCTGGCTA 3′- OGL50- SEQ ID NO: 6477 end 3PriR TCTAGCGAGAGGTGGTCAGGT UnivDonor- SEQ ID NO: 6478 3PriF1 GTTTCATCAAGCCTTACGGTCACC Nest 5′- OGL50- SEQ ID NO: 6479 PCR end 5nstPriF GCTGAAATTGCTGCATCATGGC Spec- SEQ ID NO: 6480 nstPriR1 GTTGCCTTGGTAGGTCCAGC 3′- OGL50- SEQ ID NO: 6481 end 3nstPriR AGCTGCTACATCTGTGGTCGG UnivDonor- SEQ ID NO: 6482 3PriF2 CAGCAACGTCGGTTCGAGATG OGL51 First 5′- OGL51- SEQ ID NO: 6483 PCR end 5PriF CCTTCACAGTACTTGAACTGCTGCA 3′- OGL51- SEQ ID NO: 6484  end 3PriR CACTCACATGGTGCGTTCCG Nest 5′- OGL51- SEQ ID NO: 6485 PCR end 5nstPriF TGTATGCCTCGTCATCGAGGG 3′- OGL51- SEQ ID NO: 6486 end 3nstPriR AGGGGAATGACCAGGAGCAG OGL52 First 5′- OGL52- SEQ ID NO: 6487 PCR end 5PriF TCACGTACTGACCACAGAACACC 3′- OGL52- SEQ ID NO: 6488 end 3PriR GAATATGCTCCACGCGCATCTC Nest 5′- OGL52- SEQ ID NO: 6489 PCR end 5nstPriF GCTGACTCTAAAACCGCCTTGTG 3′- OGL52- SEQ ID NO: 6490 end 3nstPriR GATCCGGCTTGTTCGCTTGAC OGL53 First 5′- OGL53- SEQ ID NO: 6491 PCR end 5PriF AACCATAGTGGCTCGCCAGT 3′- OGL53- SEQ ID NO: 6492 end 3PriR AATCGCACTAGGTCAGCATGGT Nest 5′- OGL53- SEQ ID NO: 6493 PCR end 5nstPriF GATCATGTCGTTAGCCTCCAACCA 3′- OGL53- SEQ ID NO: 6494 end 3nstPriR GTGAAGACTCGAGCTTGGCCT OGL54 First 5′- OGL54- SEQ ID NO: 6495 PCR end 5PriF2 CAACAAGCTGGTTTGCAGGGT 3′- OGL54- SEQ ID NO: 6496 end 3PriR TAACCCCCTTAGAGATGCACATGC Nest 5′- OGL54- SEQ ID NO: 6497 PCR end 5nstPriF2 ACCCCAGCAAATTGGACGATCT 3′- OGL54- SEQ ID NO: 6498 end 3nstPriR TAGATCGATGAAACCGGTCGATGTG OGL55 First 5′- OGL55- SEQ ID NO: 6499 PCR end 5PriF GACCAACCATTTGTTGCCCCT 3′- OGL55- SEQ ID NO: 6500 end 3PriR CACGTCTTTGTAGCGACTGTCCA Nest 5′- OGL55- SEQ ID NO: 6501 PCR end 5nstPriF TCCGAAAACTCAAGCATGCCC 3′- OGL55- SEQ ID NO: 6502 end 3nstPriR GTGGTGAACTTCCCTCTAGACCC OGL56 First 5′- OGL56- SEQ ID NO: 6503 PCR end 5PriF2 TGGAAAAACGTAGATGTGCTTGCC 3′- OGL56- SEQ ID NO: 6504 end 3PriR2 CAAGCTCTTTGATCGTGGTTGACG Nest 5′- OGL56- SEQ ID NO: 6505 PCR end 5nstPriF2 GCAGTAAACCTAGTGATGCTGCCT 3′- OGL56- SEQ ID NO: 6506  end 3nstPriR2 ATGCTTGGTCAACGTGCCAC OGL57 First 5′- OGL57- SEQ ID NO: 6507 PCR end 5PriF2 CGGTGAATGCAAGCTGGATCAC 3′- OGL57- SEQ ID NO: 6508 end 3PriR2 GCACTTGTGCTATCCGCCAG Nest 5′- OGL57- SEQ ID NO: 6509 PCR end 5nstPriF2 CTTTTGGTGGCGGAGATCAGG 3′- OGL57- SEQ ID NO: 6510 end 3nstPriR2 TGGAGGAGGAAATCTCTGCTATTCGT OGL58 First 5′- OGL58- SEQ ID NO: 6511 PCR end 5PriF ACAGTGGACTCCCTCGCAAG 3′- OGL58- SEQ ID NO: 6512 end 3PriR2 GTAAGCTTCCTCGACACCTCCA Nest 5′- OGL58- SEQ ID NO: 6513 PCR end 5nstPriF TCTGAAGCACAGTTTAGCCGCA 3′- OGL58- SEQ ID NO: 6514 end 3nstPriR2 GTGGTTATCTGTAGCTTGAGCACTGA OGL59 First 5′- OGL59- SEQ ID NO: 6515 PCR end 5PriF2 TGTGTTCCTTCTCCATGCACCT 3′- OGL59- SEQ ID NO: 6516 end 3PriR2 CCTTGTCACGGAGACTCTCGG Nest 5′- OGL59- SEQ ID NO: 6517 PCR end 5nstPriF2 TCACATGCCTCAACTGGAGCA 3′- OGL59- SEQ ID NO: 6518 end 3nstPriR2 TGGAAGGGCAAAACTGAGCC OGL60 First 5′- OGL60- SEQ ID NO: 6519 PCR end 5PriF GCGACCTTTTCATTGTTGGAGTAGG 3′- OGL60- SEQ ID NO: 6520  end 3PriR TACCACACCATCGAGCCGTC Nest 5′- OGL60- SEQ ID NO: 6521 PCR end 5nstPriF ACGATTCAGTAGGTAGGGTGCCT 3′- OGL60- SEQ ID NO: 6522  end 3nstPriR ACCCATTTCGAGCTGCCTGT OGL61 First 5′- OGL61- SEQ ID NO: 6523 PCR end 5PriF CCATGCAGATGTCGAGGCAAC 3′- OGL61- SEQ ID NO: 6524 end 3PriR TACTGCCTTCTGAACCGTCGG Nest 5′- OGL61- SEQ ID NO: 6525 PCR end 5nstPriF TGTTTAGCTACATCCACGGGCAT 3′- OGL61- SEQ ID NO: 6526 end 3nstPriR ACTGCAATGACAAGGCACATCC OGL62 First 5′- OGL62- SEQ ID NO: 6527 PCR end 5PriF GCACGTCGTTAGTGATCGAGCT 3′- OGL62- SEQ ID NO: 6528 end 3PriR GTTGTCAACGAAGCCCGTCTAATTG Nest 5′- OGL62- SEQ ID NO: 6529 PCR end 5nstPriF CCTGCAGTTAACGCAGACGTG 3′- OGL62- SEQ ID NO: 6530 end 3nstPriR CTAGACCGTACTATTGTGCTGTGAAG OGL63 First 5′- OGL63- SEQ ID NO: 6531 PCR end 5PriF TCCTTACTGGCCCCTAGTCCA 3′- OGL63- SEQ ID NO: 6532 end 3PriR CTCCCACGAGCGACTAGCTAC Nest 5′- OGL63- SEQ ID NO: 6533 PCR end 5nstPriF TGCAACTATGGACTTGGCCACA 3′- OGL63- SEQ ID NO: 6534 end 3nstPriR CCTCACGAATAAAAGCACCCCC OGL64 First 5′- OGL64- SEQ ID NO: 6535 PCR end 5PriF AGTCTACGTGGCATACAACCCC 3′- OGL64- SEQ ID NO: 6536 end 3PriR GAAACTTGGACCTTGCTGTCGG Nest 5′- OGL64- SEQ ID NO: 6537 PCR end 5nstPriF AGGTCTCGAACAAACTCCCTATGC 3′- OGL64- SEQ ID NO: 6538 end 3nstPriR CCATTCCATGAAGACCGACTCCA OGL65 First 5′- OGL65- SEQ ID NO: 6539 PCR end 5PriF ACCAAATCCGTTTGCTTTCACCG 3′- OGL65- SEQ ID NO: 6540 end 3PriR CTCTGACAGATACCACGTTCGCT Nest 5′- OGL65- SEQ ID NO: 6541 PCR end 5nstPriF CACCGTTTCACGAAGCTGCA 3′- OGL65- SEQ ID NO: 6542 end 3nstPriR ACCGAAATCTGCGCGCTAGTT OGL66 First 5′- OGL66- SEQ ID NO: 6543 PCR end 5PriF ACAGAAGAGGTTGCGGAGTAACG 3′- OGL66- SEQ ID NO: 6544 end 3PriR AAACAAAATCGTATCGCCGAGCAG Nest 5′- OGL66- SEQ ID NO: 6545 PCR end 5nstPriF TACTTGGACCGGCCTCTACCT 3′- OGL66- SEQ ID NO: 6546 end 3nstPriR AACCTTGCAACAGCCCCAAAT OGL67 First 5′- OGL67- SEQ ID NO: 6547 PCR end 5PriF AGGTAATACCAGTGAGCCGAC Spec- SEQ ID NO: 6548 PriR1 CCACGATCGACATTGATCTGGCTA 3′- OGL67- SEQ ID NO: 6549 end 3PriR CACTCTGTACTGGGAGAGGG UnivDonor- SEQ ID NO: 6550 3PriF1 GTTTCATCAAGCCTTACGGTCACC Nest 5′- OGL67- SEQ ID NO: 6551 PCR end 5nstPriF ATAATGCAGCGCTTGCAGAT Spec- SEQ ID NO: 6552 nstPriR2 GCTGGCGATGAGCGAAATGTAG 3′- OGL67- SEQ ID NO: 6553 end 3nstPriR CTCAATTCCATGTGCAACCAAAC UnivDonor- SEQ ID NO: 6554 3PriF2 CAGCAACGTCGGTTCGAGATG OGL68 First 5′- OGL68- SEQ ID NO: 6555 PCR end 5PriF GTGGTGATACCGTCGTCTCTCC 3′- OGL68- SEQ ID NO: 6556 end 3PriR CACTTTGTCCCTGCTCGGTTC Nest 5′- OGL68- SEQ ID NO: 6557 PCR end 5nstPriF GAAACAAGCCATTGATTGTGCCCA 3′- OGL68- SEQ ID NO: 6558 end 3nstPriR GTCGACTCACAACGCTTCCC OGL69 First 5′- OGL69- SEQ ID NO: 6559 PCR end 5PriF AGTACAACACTGAGACGTGGGC 3′- OGL69- SEQ ID NO: 6560 end 3PriR ACTAGGATTGCTAGGGAGCACGAA Nest 5′- OGL69- SEQ ID NO: 6561 PCR end 5nstPriF AGATTGCAGGGCACTTGAGGT 3′- OGL69- SEQ ID NO: 6562 end 3nstPriR ACAGGATTACAAGCCCAAACCCA OGL70 First 5′- OGL70- SEQ ID NO: 6563 PCR end 5PriF TTCTTCAGGCGGCATCGCATA Spec- SEQ ID NO: 6564 PriR1 CCACGATCGACATTGATCTGGCTA 3′- OGL70- SEQ ID NO: 6565 end 3PriR TAGTAGCCGACAATGTGGCCC UnivDonor- SEQ ID NO: 6566 3PriF1 GTTTCATCAAGCCTTACGGTCACC Nest 5′- OGL70- SEQ ID NO: 6567 PCR end 5nstPriF CGCTCAGGAAATCCTTGATGCC Spec- SEQ ID NO: 6568 nstPriR2 GCTGGCGATGAGCGAAATGTAG 3′- OGL70- SEQ ID NO: 6569 end 3nstPriR GTGAACGACGGCAACAAGCT UnivDonor- SEQ ID NO: 6570 3PriF2 CAGCAACGTCGGTTCGAGATG OGL71 First 5′- OGL71- SEQ ID NO: 6571 PCR end 5PriF GAGGTCCCTTACGGGTCATCG 3′- OGL71- SEQ ID NO: 6572 end 3PriR ACCAGGTCTATCTTGCGCAGAC Nest 5′- OGL71- SEQ ID NO: 6573 PCR end 5nstPriF AATAGCGTGGTCGGGTCCTAG 3′- OGL71- SEQ ID NO: 6574 end 3nstPriR ACGAACGATCCAAGGTGCAGT OGL72 First 5′- OGL72- SEQ ID NO: 6575 PCR end 5PriF CCAATGGACGACAGCGGTTAG 3′- OGL72- SEQ ID NO: 6576 end 3PriR ACGAGAACAAGCCACTCTTGCT Nest 5′- OGL72- SEQ ID NO: 6577 PCR end 5nstPriF CAACCGGAGAACGGATAGCCT 3′- OGL72- SEQ ID NO: 6578 end 3nstPriR TGAAGATTTCCCTACCGTCGCC OGL73 First 5′- OGL73- SEQ ID NO: 6579 PCR end 5PriF1 AGTACTGGGGACGTTCACCG 3′- OGL73- SEQ ID NO: 6580 end 3PriR1 CGACAAGAACCCGGTACATGC Nest 5′- OGL73- SEQ ID NO: 6581 PCR end 5PriF2 AGAGCTGAAACTGATCGCGGT 3′- OGL73- SEQ ID NO: 6582 end 3PriR2 GACAGAGTCCGATCCCTGCT OGL74 First 5′- OGL74- SEQ ID NO: 6583 PCR end 5PriF GCCACACGGATTTTGCGTATCA 3′- OGL74- SEQ ID NO: 6584 end 3PriR CTTTTGTCGGTCCTGCCACTG Nest 5′- OGL74- SEQ ID NO: 6585 PCR end 5nstPriF AGCAACGTAGGGTCACGGAC 3′- OGL74- SEQ ID NO: 6586 end 3nstPriR GAGGAGTCTTCGATGCCACGA OGL75 First 5′- OGL75- SEQ ID NO: 6587 PCR end 5PriF GAAAGCACCAGGTCGTATCTTGC 3′- OGL75- SEQ ID NO: 6588 end 3PriR CGCACAATCTTCGCTTCAAACCA Nest 5′- OGL75- SEQ ID NO: 6589 PCR end 5nstPriF GCATTGCTCTTCAGGAGGTACGT 3′- OGL75- SEQ ID NO: 6590 end 3nstPriR CAGCTGTGCAAGTCCGACTG OGL76 First 5′- OGL76- SEQ ID NO: 6591 PCR end 5PriF TCTCCATACCTGCACTGGGTG 3′- OGL76- SEQ ID NO: 6592 end 3PriR ACGTGCTCTCAGCAACATCCA Nest 5′- OGL76- SEQ ID NO: 6593 PCR end 5nstPriF CGTCCAAACAGGCTAGACAGC 3′- OGL76- SEQ ID NO: 6594 end 3nstPriR TGCCTTTTGCGTCAACGGTG OGL77 First 5′- OGL77- SEQ ID NO: 6595 PCR end 5PriF CCATCCAGATCGCGGTTGTC 3′- OGL77- SEQ ID NO: 6596 end 3PriR TACGAGTTCACGCCATTGCGT Nest 5′- OGL77- SEQ ID NO: 6597 PCR end 5nstPriF GTCTCCTCTTTGACGGTTGCG 3′- OGL77- SEQ ID NO: 6598 end 3nstPriR TCGATCCACACTCGCATGCA OGL78 First 5′- OGL78- SEQ ID NO: 6599 PCR end 5PriF GTGGACCAGTGTAAAGCCCG 3′- OGL78- SEQ ID NO: 6600 end 3PriR TCCCTAGTGCCAGGACCTGA Nest 5′- OGL78- SEQ ID NO: 6601 PCR end 5nstPriF ACACCAAATGTCCGGTAGCGA 3′- OGL78- SEQ ID NO: 6602 end 3nstPriR CGACGATTCTCCATTGGCCG OGL79 First 5′- OGL79- SEQ ID NO: 6603 PCR end 5PriF GCTAGAAACGCTGAACAGCAGC 3′- OGL79- SEQ ID NO: 6604 end 3PriR CGGGTTTAGAATCCACAAGCCG Nest 5′- OGL79- SEQ ID NO: 6605 PCR end 5nstPriF GACAAAAGCTGCCATCAACGCT 3′- OGL79- SEQ ID NO: 6606 end 3nstPriR CCCGATATGGACAGGTCAGCT OGL80 First 5′- OGL80- SEQ ID NO: 6607 PCR end 5PriF AAAGGCGACACACACCTTTGC 3′- OGL80- SEQ ID NO: 6608 end 3PriR AGACAGCCATCCTCACTCGC Nest 5′- OGL80- SEQ ID NO: 6609 PCR end 5nstPriF TTTGGTGCAGAGGCCGAGAA 3′- OGL80- SEQ ID NO: 6610 end 3nstPriR AAGTAGCCAGGCAGACAACCA OGL81 First 5′- OGL81- SEQ ID NO: 6611 PCR end 5PriF CTAGGCAGGGTGGCATGAAAG Spec- SEQ ID NO: 6612 PriR1 CCACGATCGACATTGATCTGGCTA 3′- OGL81- SEQ ID NO: 6613 end 3PriR ACCATCAGAGGTTGTGAAGGCA UnivDonor- SEQ ID NO: 6614 3PriF CAAATTCCCACTAAGCGCTCGG Nest 5′- OGL81- SEQ ID NO: 6615 PCR end 5nstPriF AAGGGCAACTTCATGGTTCAACC Spec- SEQ ID NO: 6616 nstPriR1 GTTGCCTTGGTAGGTCCAGC 3′- OGL81- SEQ ID NO: 6617 end 3nstPriR ACCAGTAAATCCACAACCCATGGT UnivDonor- SEQ ID NO: 6618 3nstPriF GTAAAGGTGAGCAGAGGCACG OGL03 First 5′- OGL03- SEQ ID NO: 6691 PCR end 5PriF TATATGGTGGCCAATGGACGATGG 3′- OGL03- SEQ ID NO: 6692 end 3PriR CCACAGGAGCAAGCAGTGAC Nest 5′- OGL03- SEQ ID NO: 6693 PCR end 5nstPriF CGCATCTTTGGGGGTAGTGG 3′- OGL03- SEQ ID NO: 6694 end 3nstPriR AGTACCCAGTTGGTCTCGCC

TABLE 10 List of all “In” primers for nested In-Out PCR analysis of optimal genomic loci. All 5′- Spec- SEQ ID NO: 5473 Re- end PriR1 CCACGATCGACATTG actions ATCTGGCTA First 3′- Uzi- SEQ ID NO: 5474 PCR end PriF1 GGGATATGTGTCCTA CCGTATCAGG Nest 5′- Spec- SEQ ID NO: 5475 PCR end nstPriR1 GTTGCCTTGGTAGGT CCAGC 3′- Uzi- SEQ ID NO: 5476 end nstPriF1 GAGCCATCAGTCCAA CACTGC

TABLE 11 Primers for ZFN cleavage activity. OGL 1 Control/ SEQ ID NO: 5477 ZFN 111879 TGGCACTAATCTCACCGGCT SEQ ID NO: 5478 AGTCTTAGAAGTACGCTACCGT OGL 2 Control/ SEQ ID NO: 5479 ZFN 111885 TACTTGGCTTCGGCGGCGA SEQ ID NO: 5480 GGGTGACTTTTACGCGTCTCG OGL 11 Control/ SEQ ID NO: 5481 ZFN 117402 GGTCACGACGCATGGCCTAA SEQ ID NO: 5482 AGGATGCATGGATCACCGTC OGL 12 Control/ SEQ ID NO: 5483 ZFN 117404 GCTCTGTTGTGCAGCCGTAC SEQ ID NO: 5484 CGTTGCAGATACCACAGTGTAC OGL 13 Control/ SEQ ID NO: 5485 ZFN 117429 GCTAGTAGCTGTTTACACGGCGTCT SEQ ID NO: 5486 AGGTCGAGACAACCAAGTAGAG OGL 14 Control/ SEQ ID NO: 5487 ZFN 117406 ACAGGACATCGAGCTTGCAT SEQ ID NO: 5488 CAGAAGAAAGGCATCAACTCATG OGL 15 Control/ SEQ ID NO: 5489 ZFN 117408 CTCTTTCACCTCTACTTTTACTTCAG SEQ ID NO: 5490 ATTGAACCGTTGTCAAAGCCA OGL 16 Control/ SEQ ID NO: 5491 ZFN 117411 CACAGCGTCAGGGCGGTAAC SEQ ID NO: 5492 GGCACGCACCTGTCACTGAC OGL 17 Control/ SEQ ID NO: 5493 ZFN 117413 GTACGCGCCCGGGAACTCCT SEQ ID NO: 5494 CCTGCGGCCCACGTGCATCT

Deployment of the In-Out PCR assay in a protoplast targeting system was particularly challenging as large amounts of the plasmid DNA was used for transfection, and the large amount of DNA remains in the protoplast targeting system and was subsequently extracted along with cellular genomic DNA. The residual plasmid DNA may dilute the relative concentration of the genomic DNA and reduce the overall sensitivity of detection and can also be a significant cause of non-specific, aberrant PCR reactions. ZFN induced NHEJ-based donor insertion typically occurs in either a forward or a reverse orientation. In-Out PCR analysis of DNA for the forward orientation insertion often exhibited false positive bands, possibly due to shared regions of homology around the ZFN binding site in the target and donor that could result in priming and extension of unintegrated donor DNA during the amplification process. False positives were not seen in analyses that probed for reverse orientation insertion products and therefore all targeted donor integration analysis was carried out to interrogate reverse donor insertion in the RTA. In order to further increase specificity and reduce background, a nested PCR strategy was also employed. The nested PCR strategy used a second PCR amplification reaction that amplified a shorter region within the first amplification product of the first PCR reaction. Use of asymmetric amounts of “in” and “out” primers optimized the junctional PCR further for rapid targeting analysis at selected genomic loci.

The In-Out PCR analysis results were visualized on an agarose gel. For all Zea mays selected genomic loci of Table 12, “ZFN+donor treatments” produced a near expected sized band at the 5′ and 3′ ends. Control ZFN or donor alone treatments were negative in the PCR suggesting that the method was specifically scoring for donor integration at the target site of at least 72 of the optimal nongenic maize genomic loci. All treatments were conducted in replicates of 3-6 and presence of the anticipated PCR product in multiple replicates (>2 at both ends) was used to confirm targeting. Donor insertion through NHEJ often produces lower intensity side products that were generated due to processing of linearized ends at the target and/or donor ZFN sites. In addition, it was observed that different ZFNs resulted in different levels of efficiency for targeted integration, with some of the ZFNs producing consistently high levels of donor integration, some ZFNs producing less consistent levels of donor integration, and other ZFNs resulting in no integration. Overall, for each of the Zea mays selected genomic loci targets that were tested, targeted integration was demonstrated within the Zea mays representative genomic loci targets by one or more ZFNs, which confirms that each of these loci were targetable. Furthermore, each of the Zea mays selected genomic loci targets was suitable for precision gene transformation. The validation of these Zea mays selected genomic loci targets was repeated multiple times with similar results every time, thus confirming the reproducibility of the validation process which includes plasmid design and construct, protoplast transformation, sample processing, and sample analysis.

Conclusion

The donor plasmid and one ZFN designed to specifically cleave a Zea mays selected genomic loci targets were transfected into Zea mays c.v. Hi-II protoplasts and cells were harvested 24 hours later. Analysis of the genomic DNA isolated from control, ZFN treated and ZFN with donor treated protoplasts by in-out junctional PCR showed targeted insertion of the universal donor polynucleotide as a result of genomic DNA cleavage by the ZFNs (Table 12). These studies show that the universal donor polynucleotide system can be used to assess targeting at endogenous sites and for screening candidate ZFNs. Finally, the protoplast based Rapid Targeting Analysis and the novel universal donor polynucleotide sequence systems provide a rapid avenue for screening genomic targets and ZFNs for precision genome engineering efforts in plants. The methods can be extended to assess site specific cleavage and donor insertion at genomic targets in any system of interest using any nuclease that introduces DNA double or single strand breaks.

TABLE 12 Illustrates the results of the integration of a universal donor polynucleotide sequence within the Zea mays selected genomic loci targets. As indicated by the * below, donor insertion within OGL73 was only confirmed by a PCR reaction of the 5′ junction sequence. Targetable Cluster ZFN Donor Locus Name ID Location Assignment (pDAB#) (pDAB#) (Y/N) OGL01 optimal_loci_204637_G1 chr5: 200298202 . . . 200301414 16 111879 111845 Y OGL02 optimal_loci_204726_G1 chr5: 200665730 . . . 200670667 03 111885 111846 Y OGL08 optimal_loci_31710 chr1: 194939396 . . . 194943360 23 117400 117415 Y OGL11 optimal_loci_64542 chr2: 72203716 . . . 72205045 14 117402 117416 Y OGL12 optimal_loci_156393 chr4: 154313884 . . . 154315253 10 117404 117417 Y OGL15 preffered_loci_198387 chr5: 164712378 . . . 164713567 25 117408 117419 Y OGL13 optimal_loci_157315 chr4: 158710709 . . . 158711983 30 117429 117434 Y OGL14 optimal_loci_197372 chr5: 158680601 . . . 158681681 26 117406 117418 Y OGL16 optimal_loci_232228 chr6: 144719567 . . . 144723469 28 117411 117420 Y OGL17 optimal_loci_285621 chr8: 118321357 . . . 118322528 06 117413 117421 Y OGL04 optimal_loci_43577 chr1: 256469704 . . . 256472666 20 124802 124812 Y OGL05 optimal_loci_301774 chr9: 23468085 . . . 23470278 15 121900 121926 Y OGL06 optimal_loci_232222 chr6: 144700575 . . . 144702126 20 124810 124813 Y OGL07 optimal_loci_203704 chr5: 194836270 . . . 194840217 12 121902 121930 Y OGL09 optimal_loci_59517 chr2: 43352132 . . . 43353146 1 118643 118697 Y OGL10 optimal_loci_25001 chr1: 151371224 . . . 151372260 1 118648 118686 Y OGL18 optimal_loci_112632 chr3: 128098856 . . . 128100257 2 123802 123810 Y OGL19 optimal_loci_28905 chr1: 177037718 . . . 177038919 2 123805 123809 Y OGL20 optimal_loci_129164 chr3: 221246027 . . . 221247542 3 121992 123808 Y OGL21 optimal_loci_2425 chr1: 12810845 . . . 12814490 3 118650 118697 Y OGL22 optimal_loci_122036 chr3: 184608166 . . . 184609697 4 118654 118688 Y OGL23 optimal_loci_5735 chr1: 29190279 . . . 29192844 4 118656 118689 Y OGL24 optimal_loci_178978 chr5: 35776311 . . . 35777560 5 118659 118690 Y OGL25 optimal_loci_288388 chr8: 133290442 . . . 133291481 5 118660 118697 Y OGL26 optimal_loci_60310 chr2: 47967092 . . . 47968271 5 118767 118787 Y OGL27 optimal_loci_243330 chr7: 34630402 . . . 34631577 6 118769 118787 Y OGL28 optimal_loci_127038 chr3: 210603611 . . . 210605198 7 118663 118697 Y OGL29 optimal_loci_262784 chr7: 155767046 . . . 155769049 7 118668 118691 Y OGL30 optimal_loci_344662 chr10: 119131667 . . . 119133955 7 118669 118692 Y OGL31 optimal_loci_153894 chr4: 139979597 . . . 139981225 8 118670 118693 Y OGL32 optimal_loci_28771 chr1: 176062139 . . . 176063611 8 118673 118694 Y OGL33 optimal_loci_1098 chr1: 5582601 . . . 5583834 9 118674 118695 Y OGL34 optimal_loci_97772 chr3: 30209253 . . . 30210607 9 118676 118696 Y OGL35 optimal_loci_236662 chr6: 165975716 . . . 165977010 10 118677 118697 Y OGL36 optimal_loci_139485 chr4: 42804231 . . . 42805751 11 118680 118697 Y OGL37 optimal_loci_301175 chr9: 20325171 . . . 20326621 11 118683 118764 Y OGL38 optimal_loci_152337 chr4: 130033092 . . . 130035481 12 118685 118765 Y OGL39 optimal_loci_202616 chr5: 188822901 . . . 188824814 12 123833 123809 Y OGL40 optimal_loci_282323 chr8: 100763204 . . . 100764398 13 118771 118787 Y OGL41 optimal_loci_262782 chr7: 155759080 . . . 155760097 13 121943 121983 Y OGL42 optimal_loci_236455 chr6: 164795991 . . . 164797027 14 121946 121984 Y OGL43 optimal_loci_162531 chr4: 189896984 . . . 189899332 15 121949 121985 Y OGL44 optimal_loci_344663 chr10: 119143167 . . . 119144795 15 121952 121986 Y OGL45 optimal_loci_337001 chr10: 77188319 . . . 77190007 16 121959 121987 Y OGL46 optimal_loci_238100 chr7: 4899227 . . . 4900708 16 121963 121988 Y OGL48 optimal_loci_264359 chr7: 163504241 . . . 163505487 17 121971 121990 Y OGL49 optimal_loci_282653 chr8: 102704765 . . . 102705924 18 121972 121991 Y OGL50 optimal_loci_80282 chr2: 173420834 . . . 173421870 18 124097 124295 Y OGL51 optimal_loci_291068 chr8: 148277606 . . . 148279985 19 123818 123831 Y OGL52 optimal_loci_56395 chr2: 24801482 . . . 24803132 19 118705 121201 Y OGL54 optimal_loci_114664 chr3: 140106950 . . . 140108061 21 118711 118792 Y OGL57 optimal_loci_53137 chr2: 7304197 . . . 7305496 22 118718 118794 Y OGL58 optimal_loci_344664 chr10: 119144946 . . . 119146850 23 118722 121208 Y OGL59 optimal_loci_81941 chr2: 181418576 . . . 181421181 24 118726 121209 Y OGL60 optimal_loci_321514 chr9: 140776147 . . . 140777584 24 118728 121210 Y OGL61 optimal_loci_301180 chr9: 20328932 . . . 20330129 25 118732 121211 Y OGL62 optimal_loci_348776 chr10: 142097590 . . . 142098803 26 118733 121212 Y OGL63 optimal_loci_244439 chr7: 41068791 . . . 41070248 27 118735 118795 Y OGL64 optimal_loci_348258 chr10: 139297032 . . . 139298517 27 118739 121214 Y OGL65 optimal_loci_322501 chr9: 146078534 . . . 146080201 28 118742 121215 Y OGL66 optimal_loci_244324 chr7: 40299412 . . . 40300584 29 118745 121216 Y OGL67 optimal_loci_97232 chr3: 27463016 . . . 27464143 29 124081 124866 Y OGL68 optimal_loci_282499 chr8: 101771408 . . . 101772767 30 125361 125366 Y OGL69 optimal_loci_155031 chr4: 146991391 . . . 146993137 31 118753 121218 Y OGL70 optimal_loci_301773 chr9: 23465509 . . . 23467762 31 124878 123880 Y OGL71 optimal_loci_283161 chr8: 105321958 . . . 105323571 32 123829 123832 Y OGL72 optimal_loci_55524 chr2: 20099003 . . . 20100485 32 118761 121221 Y OGL73 optimal_loci_127268 chr3: 211767898 . . . 211770046 16 124086 124298 Y* OGL74 optimal_loci_137693 chr4: 31118968 . . . 31122359 3 121904 121927 Y OGL75 optimal_loci_265551 chr7: 170127188 . . . 170130734 3 121905 121927 Y OGL76 optimal_loci_128078 chr3: 215482594 . . . 215485640 4 121917 121927 Y OGL77 optimal_loci_168286 chr4: 219987223 . . . 219990695 4 121918 121928 Y OGL78 optimal_loci_3733 chr1: 19232372 . . . 19235997 11 121909 121930 Y OGL79 optimal_loci_203075 chr5: 191370802 . . . 191374627 12 121912 121929 Y OGL80 optimal_loci_232484 chr6: 146122164 . . . 146125580 12 121981 121936 Y OGL81 optimal_loci_136086 chr4: 22531506 . . . 22534989 27 124091 124298 Y

Example 7: Expression of Polynucleotide Donor Sequence within the Genomic Loci of Zea mays

Randomly integrated maize transformation events were generated by transformation with the pDAB105817 and pEPS1027 plasmids containing the aad-1 transgene, described in U.S. Pat. No. 7,838,733. (FIG. 14). Large numbers of events were produced and 1,027 stable events were analyzed to determine if any of the events contained a randomly integrated transgene within the Zea mays selected genomic loci targets via a genome flanking analysis method as described in U.S. Patent Application No. 2012/0258867. As such, the chromosomal location of the integrated transgene in 223 events was mapped within the Zea mays genome. The data, Table 13, indicated that the chromosomal location of the integrated transgenes demonstrated integration within hypomethylated regions (45-73%) and in transcriptional units (promoter/gene/3′UTR) downstream of at least 1 Kb areas (60%).

TABLE 13 Genomic and epigenomic context of the 1027 mapped events. No. events No. of total mapped with No. events mapped number of high confidence with low confidence events Count 107 116 223 100 bp 102 61 163 hypomethylated regions 2 kb 68 27 95 hypomethylated regions Gene body 45 26 71 Upstream 2 kb 32 11 43 Downstream 1 kb 16 3 19 Repeat 9 62 71 Total 88 98 186 genic/repeat

The mapped events were further analyzed using the optimal locus predictive criteria described in Examples 1 and 2 (hypomethylated regions, unique regions, nongenic, non-repeat, proximal to genes in a 40 Kb neighborhood, evidence of active expression in roots/shoots, evidence of recombination) and several randomly integrated events were identified within the Zea mays selected genomic loci targets (Table 14). For example, targeting within the Zea mays selected genomic loci targets optimal_loci_232222 and optimal_loci_127268 have been demonstrated using Rapid Testing Analysis and by in planta targeting, respectively.

The average length of the experimental Zea mays selected genomic loci targets were approximately 1 Kb and varying degrees of aad-1 expression was observed at each of the Zea mays selected genomic loci targets (Table 14). The average aad-1 expression analysis was conducted at the T₁ plant transformation stage via a real-time PCR analysis of isolated transgenic leaf material. As such, random integration events within the Zea mays genome were capable of expressing a transgene within the experimental Zea mays selected genomic loci targets.

TABLE 14 Expression of the aad-1 transgene in randomly integrated within the optimal genomic loci. The Location, Length and RNA expression for the aad-1 marker gene at the locus are shown. Optimal AAD1 RNA Genomic Loci SEQ ID Expression Avg Event ID Name NO: Location Length T/R G3_PL2863_1027- optimal_loci_43565 655 chr1: 256293759 . . . 256295777 2018 22.687 nstPri3 H4_PL2783_1027- optimal_loci_164397 4552 chr4: 199185401 . . . 199186813 1413 32.825 nstPri3 B6_PL2955_1027- optimal_loci_232222 3357 chr6: 144700575 . . . 144702126 1553 3.1805 nstPri3 E7_PL3018_1027- optimal_loci_125749 19 chr3: 204456962 . . . 204458140 1179 0.5185 nstPri3 E4_PL2955_1027- optimal_loci_7953 1777 chr1: 41279823 . . . 41280909 1087 4.0805 nstPri3 A7_PL2746_1027- optimal_loci_205643 2037 chr5: 205773760 . . . 205775465 1705 1.3761 nstPri3 F4_PL2978_1027- optimal_loci_201819 2726 chr5: 184470152 . . . 184471958 1807 0.56075 nstPri3 B8_PL2955_1027- optimal_loci_42519 1929 chr1: 250905847 . . . 250908881 3035 0.4591 nstPri3 B104/pDAB105817{1}015.001-1 optimal_loci_127268 2709 chr3: 211,767,898 . . . 211,770,046 2149 1.54

Example 8: Optimal Nongenic Maize Genomic Loci for Transgene Integration

A suite of optimal nongenic maize genomic loci were identified from the 5,286 optimal nongenic maize genomic loci to select multiple loci for site specific targeting of gene expression cassettes and to generate stacks of gene expression cassettes. The following criteria were used to filter the pool of optimal nongenic maize genomic loci and select a suite of optimal nongenic maize genomic loci:

-   -   1) Greater than 3 Kb in length. The optimal nongenic maize         genomic loci can be targeted with the integration of at least         two sets of gene expression cassettes.     -   2) Recombination frequency of 0.5 to 1.0, which is less than the         average recombination frequency of the identified 5,286 optimal         nongenic maize genomic loci (average recombination frequency is         about 2.0).     -   3) Greater than average expression of endogenous genes within 40         Kb of the identified 5,286 optimal nongenic maize genomic loci.         Average expression of genes within a 40 Kb region in root and         shoot tissues is greater than 6.30, which is the 48th percentile         of all optimal nongenic maize genomic loci.     -   4) Sequence coverage and sequence identity of greater than 90%         between Zea mays c.v. B104 and Zea mays c.v. Hi-II.         Each of the above described criteria were applied to select a         suite of optimal nongenic maize genomic loci. FIG. 24 provides         three illustrative diagrams of the criteria, and how the         selected optimal nongenic maize genomic loci compared in         relation to other loci. Nine optimal nongenic maize genomic loci         (optimal_loci_137693_G1, optimal_loci_265551_G1,         optimal_loci_128078_G1, optimal_loci_168286_G1,         optimal_loci_3733_G1, optimal_loci_203075_G1,         optimal_loci_232484_G1, optimal_loci_136086_G1, and         optimal_loci_203704_G1) that were at least 3 Kb in length were         identified using this criteria. See Table 15. Additional optimal         nongenic maize genomic loci were identified by reducing the size         limitation to >2 Kb (optimal_loci_291068_G1, and         optimal_loci_43577_G1), these loci were added to the suite of         optimal nongenic maize genomic loci. Another set of optimal         nongenic maize genomic loci were added to the suite of optimal         nongenic maize genomic loci as there was evidence of expression         of a randomly integrated transgene via Agrobacterium         transformation at these sites (optimal_loci_232222_G1 and         optimal_loci_127268_G1). The optimal_loci_204637_G1 and         optimal_loci_204726_G1 genomic loci were added to the suite for         their meiotic recombination unit features. In addition,         optimal_loci_204637_G1 and optimal_loci_204726_G1 have been         successfully targeted for integration of a donor polynucleotide.         Likewise, optimal_loci_232228 was included in the suite as this         optimal nongenic maize genomic loci has been successfully         targeted for integration of a donor polynucleotide, and the         length of the sequence is 3.9 Kb.

Next, all of the optimal nongenic maize genomic loci were characterized for distance to proximal genes and distance from centromere (FIG. 25). The suite of select optimal nongenic loci are about 1-15 Kb away from proximal genes and are located towards the end of chromosomes (distance >0.70 from centromeres) (Table 16, FIG. 25). Finally, interference by quantitative trait loci was probed to fully characterize the suite of optimal nongenic maize genomic loci.

TABLE 15 Suite of optimal nongenic maize genomic loci. SEQ ID OGL_ID Location Length NO: optimal_loci_203704_G1 chr5: 194836270 . . . 3948 2033 194840217 optimal_loci_291068_G1 chr8: 148277606 . . . 2380 3230 148279985 optimal_loci_43577_G1 chr1: 256469704 . . . 2963 3428 256472666 optimal_loci_232222_G1 chr6: 144700575 . . . 1552 3357 144702126 optimal_loci_204637_G1 chr5: 200298202 . . . 3213 2731 200301414 optimal_loci_204726_G1 chr5: 200665730 . . . 4938 424 200670667 optimal_loci_232228_G1 chr6: 144719567 . . . 3902 4529 144723469 optimal_loci_127268_G1 chr3: 211767898 . . . 2149 2709 211770046 optimal_loci_136086_G1 chr4: 22531506 . . . 3484 4425 22534989 optimal_loci_232484_G1 chr6: 146122164 . . . 3417 2053 146125580 optimal_loci_203075_G1 chr5: 191370802 . . . 3826 2030 191374627 optimal_loci_3733_G1 chr1: 19232372 . . . 3626 1923 19235997 optimal_loci_168286_G1 chr4: 219987223 . . . 3473 573 219990695 optimal_loci_128078_G1 chr3: 215482594 . . . 3047 560 215485640 optimal_loci_265551_G1 chr7: 170127188 . . . 3547 463 170130734 optimal_loci_137693_G1 chr4: 31118968 . . . 3392 387 31122359

TABLE 16 Optimal nongenic maize genomic loci characteristics. Distance to Distance to OGL ID closest gene centromere optimal_loci_137693_G1 4070 .70444101 optimal_loci_265551_G1 9252 .94191056 optimal_loci_128078_G1 2491 .87326872 optimal_loci_168286_G1 1710 .84128147 optimal_loci_3733_G1 14910 .856875 optimal_loci_203075_G1 1001 .75612998 optimal_loci_232484_G1 1001 .80656755 optimal_loci_136086_G1 4381 .7859925 optimal_loci_203704_G1 2001 .788019 optimal_loci_127268_G1 2758 .84500724 optimal_loci_204637_G1 2874 .83827931 optimal_loci_291068_G1 4243 .77879798 optimal_loci_232222_G1 2832 .79463887 optimal_loci_43577_G1 2001 .73018748 optimal_loci_204726_G1 11370 .84166127

The optimal nongenic maize genomic loci that are selected using the above described criteria are validated by integrating a gene expression construct that contains selectable/reportable markers. This gene expression cassette is stably integrated into maize plants via genomic targeting using a site specific nuclease. The targeted optimal nongenic maize genomic loci that are produced and contain an expressible transgene are analyzed to identify single copy events that contain a full length integrated gene expression cassette. The expression profiles of the optimal nongenic maize genomic loci are analyzed via qRT-PCR, Western blot, ELISA, LC-MS MS, and other known RNA or protein detection methods over multiple plant generations (e.g., T₁ and T₂ generations). In addition, the effect of the transgene expression cassette integration within the optimal nongenic maize genomic loci on neighboring gene expression is assayed. Finally, the effect of the transgene expression cassette integration within the optimal nongenic maize genomic loci on agronomic properties of maize plants is assayed. 

The invention claimed is:
 1. A recombinant maize plant cell produced by the following steps: a. providing a maize plant cell wherein said cell comprises a target nongenic maize genomic nucleic acid molecule, said nongenic maize genomic nucleic acid molecule comprises a nongenic maize genomic nucleic acid molecule of at least 1 Kb, wherein b. the level of methylation of said nongenic maize genomic nucleic acid molecule is 1% or less; c. the nongenic maize genomic nucleic acid molecule shares less than 40% sequence identity with any other nucleic acid molecules contained in the maize genome; d. the nongenic maize genomic nucleic acid molecule is located within a 40 Kb region of a known or predicted expressive maize coding nucleic acid molecule; and e. the nongenic maize genomic nucleic acid molecule exhibits a recombination frequency within the maize genome of greater than 0.00041 cM/Mb, wherein said nongenic nucleic acid molecule has at least 95% sequence identity with a sequence selected from the group consisting of SEQ ID NO:387, identified as loci_137693_G1, SEQ ID NO:463, identified as loci_265551_G1, SEQ ID NO:560, identified as loci_128078_G1, SEQ ID NO:573, identified as loci_168286_G1, SEQ ID NO:1268, identified as loci_3733_G1, SEQ ID NO:2030, identified as loci_203075_G1, SEQ ID NO:2053, identified as loci_232484_G1, and SEQ ID NO:4529, identified as loci_232228_G1; f. selecting a site specific nuclease that specifically binds and cleaves said target nongenic maize genomic nucleic acid molecule; g, introducing said site specific nuclease activity into said maize plant cell; h. introducing a DNA of interest into the maize plant cell, wherein the DNA of interest comprises a non-native exogenous sequence; i. inserting the DNA of interest into said target nongenic maize genomic nucleic acid molecule; and, j. selecting transgenic maize plant cells comprising the DNA of interest targeted to said nongenic nucleic acid molecule.
 2. A maize plant regenerated from the maize plant cell of claim
 1. 3. A seed or other maize plant part of the plant of claim 2, wherein the maize seed or plant part comprises said DNA of interest inserted into said nongenic nucleic acid molecule.
 4. The maize plant cell of claim 1 wherein the site specific nuclease is selected from the group consisting of Zinc Finger Nucleases (ZFNs), Meganucleases, Transcription Activator-Like Effector Nucleases (TALENS) and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated nuclease and the DNA of interest is inserted within 1.5 Kb, 1.25 Kb, 1.0 Kb, 0.75 Kb, 0.5 Kb, or 0.25 Kb of a target site of said site specific nuclease.
 5. The maize plant cell of claim 1 wherein the site specific nuclease is a Zinc Finger Nuclease and said DNA of interest is inserted within 1.5 Kb, 1.25 Kb, 1.0 Kb, 0.75 Kb, 0.5 Kb, or 0.25 Kb of a zinc finger target site.
 6. The maize plant cell of claim 5, wherein said DNA of interest is inserted between a pair of zinc finger target sites.
 7. The maize plant cell of claim 1 wherein the DNA of interest comprises a gene expression cassette.
 8. The maize plant cell of claim 7 wherein the gene expressions cassette comprises an insecticidal resistance gene, herbicide tolerance gene, nitrogen use efficiency gene, water use efficiency gene, nutritional quality gene, DNA binding gene, or selectable marker gene.
 9. A maize plant, maize plant part, or maize plant cell comprising a recombinant nucleic acid molecule, said recombinant nucleic acid molecule comprises a nongenic nucleic acid molecule of at least 1 Kb, wherein a. the level of methylation of said nongenic nucleic acid molecule is 1% or less; b. the nongenic nucleic acid molecule shares less than 40% sequence identity with any other nucleic acid molecules contained in the maize genome; c. the nongenic nucleic acid molecule is located within a 40 Kb region of a known or predicted expressive maize coding nucleic acid molecule; and d. the nongenic nucleic acid molecule exhibits a recombination frequency within the maize genome of greater than 0.00041 cM/Mb, wherein said nongenic nucleic acid molecule has at least 95% sequence identity with a nongenic nucleic acid molecule selected from the group consisting of: SEQ ID NO:387, identified as loci_137693_G1, SEQ ID NO:463, identified as loci_265551_G1, SEQ ID NO:560, identified as loci_128078_G1, SEQ ID NO:573, identified as loci_168286_G1, SEQ ID NO:1268, identified as loci_3733_G1, SEQ ID NO:2030, identified as loci_203075_G1, SEQ ID NO:2053, identified as loci_232484_G1, and SEQ ID NO:4529, identified as loci_232228_G1; and a DNA of interest, wherein the DNA of interest comprises an insecticidal resistance gene or a herbicide tolerance gene and said DNA of interest is inserted into said nongenic nucleic acid molecule to produce said recombinant nucleic acid molecule.
 10. The maize plant, maize plant part, or maize plant cell of claim 9 wherein said nongenic nucleic acid molecule comprises a nongenic nucleic acid molecule selected from the group consisting of: SEQ ID NO:387, identified as loci_137693_G1, SEQ ID NO:463, identified as loci_265551_G1, SEQ ID NO:560, identified as loci_128078_G1, SEQ ID NO:573, identified as loci_168286_G1, SEQ ID NO:1268, identified as loci_3733_G1, SEQ ID NO:2030, identified as loci_203075_G1, SEQ ID NO:2053, identified as loci_232484_G1, and SEQ ID NO:4529, identified as loci_232228_G1.
 11. The maize plant, maize plant part, or maize plant cell of claim 9 wherein the nongenic maize genomic nucleic acid molecule has at least 95% sequence identity with a nucleic acid molecule selected from the group consisting of: SEQ ID NO:2053, identified as optimal_loci_232484, SEQ ID NO:2030, identified as optimal_loci_203075, SEQ ID NO:1268, identified as optimal_loci_3733, SEQ ID NO:573, identified as optimal_loci_168286, SEQ ID NO:560, identified as optimal_loci_128078, and SEQ ID NO:463, identified as optimal_loci_265551.
 12. The maize plant, maize plant part, or maize plant cell of claim 9 wherein the nongenic maize genomic nucleic acid molecule has at least 95% sequence identity with a nucleic acid molecules selected from the group consisting of SEQ ID NO:2053, identified as optimal_loci_232484, SEQ ID NO:2030, identified as optimal_loci_203075, SEQ ID NO:1268, identified as optimal_loci_3733, SEQ ID NO:573, identified as optimal_loci_168286, SEQ ID NO:560, identified as optimal_loci_128078 and SEQ ID NO:463, identified as optimal_loci_265551.
 13. The maize plant cell of claim 9 wherein said DNA of interest comprises an insecticidal resistance gene and a herbicide tolerance gene.
 14. A maize plant, maize plant part, or maize plant cell comprising a nucleic acid molecule encoding a site specific nuclease, wherein the site specific nuclease is selected from the group consisting of a zinc finger nuclease, a CRISPR nuclease, a TALEN, a homing endonuclease and a meganuclease, that specifically binds and cleaves a target nongenic maize genomic nucleic acid molecule, said target nongenic maize genomic nucleic acid molecule comprises a target nongenic maize genomic nucleic acid molecule of at least 1 Kb, wherein a. the level of methylation of said target nongenic maize genomic nucleic acid molecule is 1% or less; b. the target nongenic maize genomic nucleic acid molecule shares less than 40% sequence identity with any other nucleic acid molecules contained in the maize genome; c. the target nongenic maize genomic nucleic acid molecule is located within a 40 Kb region of a known or predicted expressive maize coding nucleic acid molecule; and d. the target nongenic maize genomic nucleic acid molecule exhibits a recombination frequency within the maize genome of greater than 0.00041 cM/Mb, wherein said target nongenic nucleic acid molecule is selected from the group consisting of SEQ ID NO:387, identified as loci_137693_G1, SEQ ID NO:463, identified as loci_265551_G1, SEQ ID NO:560, identified as loci_128078_G1, SEQ ID NO:573, identified as loci_168286_G1, SEQ ID NO:1268, identified as loci_3733_G1, SEQ ID NO:2030, identified as loci_203075_G1, SEQ ID NO:2053, identified as loci_232484_G1, and SEQ ID NO:4529, identified as loci_232228_G1.
 15. The maize plant, maize plant part, or maize plant cell of claim 14 wherein said target nongenic maize genomic nucleic acid molecule is selected from the group consisting of SEQ ID NO:560, identified as optimal_loci_128078 and SEQ ID NO:463, identified as optimal_loci_265551.
 16. The maize plant, maize plant part, or maize plant cell of claim 14 wherein the site specific nuclease is selected from the group consisting of Zinc Finger Nucleases (ZFNs), Transcription Activator-Like Effector Nucleases (TALENS) and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated nuclease.
 17. The maize plant, maize plant part, or maize plant cell of claim 16 wherein the nucleic acid molecule encoding the site specific nuclease is operably linked to an inducible promoter.
 18. The maize plant, maize plant part, or maize plant cell of claim 16 wherein the nucleic acid molecule encoding the site specific nuclease is operably linked to a constitutive promoter.
 19. The recombinant maize plant cell of claim 1 wherein said cell is produced by the following steps: a. introducing into a maize plant cell a site specific nuclease activity that specifically binds and cleaves a target nongenic maize genomic nucleic acid molecule having at least 95% sequence identity with SEQ ID NO:387; b. introducing a DNA of interest into said maize plant cell; c. inserting the DNA of interest into said target nongenic maize genomic nucleic acid molecule having at least 95% sequence identity with SEQ ID NO:387; and, d. selecting transgenic maize plant cells comprising the DNA of interest inserted into said target nongenic maize genomic nucleic acid molecule having at least 95% sequence identity with SEQ ID NO:387. 